1KNW

Crystal structure of diaminopimelate decarboxylase

PDB DOI: https://doi.org/10.2210/pdb1KNW/pdb

Classification: LYASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2001-12-19 Released: 2003-11-11
Deposition Author(s): Levdikov, V., Blagova, L., Bose, N., Momany, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.220
R-Value Work: 0.173

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Diaminopimelate Decarboxylase uses a Versatile Active Site for Stereospecific Decarboxylation

Levdikov, V., Blagova, L., Bose, N., Momany, C.

To be published.

Macromolecule Content

Total Structure Weight: 47.47 kDa
Atom Count: 3,702
Modelled Residue Count: 421
Deposited Residue Count: 425
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase	A	425	Escherichia coli	Mutation(s): 0 Gene Names: LysA EC: 4.1.1.20
UniProt
Find proteins for P00861 (Escherichia coli (strain K12)) Explore P00861 Go to UniProtKB: P00861
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00861
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain F [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A]
LI Query on LI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.220
R-Value Work: 0.173
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.58	α = 90
b = 98.58	β = 90
c = 176.95	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-11-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-11-11
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance

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Help and Resources

1KNW

Crystal structure of diaminopimelate decarboxylase

Diaminopimelate Decarboxylase uses a Versatile Active Site for Stereospecific Decarboxylation

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)