1YPN

REDUCED FORM HYDROXYMETHYLBILANE SYNTHASE (K59Q MUTANT) CRYSTAL STRUCTURE AFTER 2 HOURS IN A FLOW CELL DETERMINED BY TIME-RESOLVED LAUE DIFFRACTION

PDB DOI: https://doi.org/10.2210/pdb1YPN/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 1998-06-26 Released: 1999-03-02
Deposition Author(s): Helliwell, J.R., Nieh, Y.P., Raftery, J., Cassetta, A., Habash, J., Carr, P.D., Ursby, T., Wulff, M., Thompson, A.W., Niemann, A.C., Haedener, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.290
R-Value Work: 0.199
R-Value Observed: 0.199

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Time-Resolved Structures of Hydroxymethylbilane Synthase (Lys59Gln Mutant) as It Isloaded with Substrate in the Crystal Determined by Laue Diffraction

Helliwell, J.R., Nieh, Y.P., Cassetta, A., Habash, J., Carr, P.D., Ursby, T., Wulff, M., Thompson, A.W., Niemann, A.C., Haedener, A.

(1998) J Chem Soc Faraday Trans 94: 2615-2622

DOI: https://doi.org/10.1039/A802217H

Macromolecule Content

Total Structure Weight: 34.31 kDa
Atom Count: 2,357
Modelled Residue Count: 294
Deposited Residue Count: 313
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROXYMETHYLBILANE SYNTHASE	A	313	Escherichia coli	Mutation(s): 1 EC: 2.5.1.61
UniProt
Find proteins for P06983 (Escherichia coli (strain K12)) Explore P06983 Go to UniProtKB: P06983
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06983
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DPM Query on DPM 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]	3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid C₂₀ H₂₄ N₂ O₈ LCAXMKQKEYTFDM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.290
R-Value Work: 0.199
R-Value Observed: 0.199
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.47	α = 90
b = 76.15	β = 90
c = 50.79	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DARESBURY	data reduction
LAUENORM	data scaling
CCP4	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1999-03-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-03-02
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2013-09-18
Changes: Non-polymer description
Version 1.4: 2021-11-03
Changes: Database references, Derived calculations, Other
Version 1.5: 2023-08-09
Changes: Refinement description