2YPN | pdb_00002ypn

Hydroxymethylbilane synthase

PDB DOI: https://doi.org/10.2210/pdb2YPN/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1999-01-11 Released: 1999-02-02
Deposition Author(s): Nieh, Y.P., Raftery, J., Weisgerber, S., Habash, J., Schotte, F., Ursby, T., Wulff, M., Haedener, A., Campbell, J.W., Hao, Q., Helliwell, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.269 (Depositor)
R-Value Work:
0.194 (Depositor), 0.181 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Accurate and highly complete synchrotron protein crystal Laue diffraction data using the ESRF CCD and the Daresbury Laue software

Nieh, Y.P., Raftery, J., Weisgerber, S., Habash, J., Schotte, F., Ursby, T., Wulff, M., Haedener, A., Campbell, J.W., Hao, Q., Helliwell, J.R.

(1999) J Synchrotron Radiat 6: 995-1006

Macromolecule Content

Total Structure Weight: 34.31 kDa
Atom Count: 2,408
Modeled Residue Count: 294
Deposited Residue Count: 313
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HYDROXYMETHYLBILANE SYNTHASE)	A	313	Escherichia coli	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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: 0.269 (Depositor)
R-Value Work: 0.194 (Depositor), 0.181 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.06	α = 90
b = 75.73	β = 90
c = 50.35	γ = 90

Software Package:

Software Name	Purpose
DARESBURY	data collection
LAUENORM/AGROVATA	data reduction
X-PLOR	model building
O	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

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Entry History

Deposition Data

Released Date: 1999-02-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-02-02
Type: Initial release
Version 1.1: 2008-04-26
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: 2017-10-04
Changes: Refinement description
Version 1.5: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description