2VI8 | pdb_00002vi8

Crystal structure of S172AbsSHMT internal aldimine

PDB DOI: https://doi.org/10.2210/pdb2VI8/pdb

Classification: TRANSFERASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2007-11-28 Released: 2007-12-18
Deposition Author(s): Rajaram, V., Bhavani, B.S., Prakash, V., Appaji Rao, N., Savithri, H.S., Murthy, M.R.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.208 (Depositor), 0.205 (DCC)
R-Value Work:
0.182 (Depositor), 0.179 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of S172Absshmt and its Complexes

Rajaram, V., Bhavani, B.S., Prakash, V., Appaji Rao, N., Savithri, H.S., Murthy, M.R.N.

To be published.

Macromolecule Content

Total Structure Weight: 44.84 kDa
Atom Count: 3,651
Modeled Residue Count: 405
Deposited Residue Count: 405
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE HYDROXYMETHYLTRANSFERASE	A	405	Geobacillus stearothermophilus	Mutation(s): 1 EC: 2.1.2.1
UniProt
Find proteins for Q7SIB6 (Geobacillus stearothermophilus) Explore Q7SIB6 Go to UniProtKB: Q7SIB6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SIB6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP 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]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.208 (Depositor), 0.205 (DCC)
R-Value Work: 0.182 (Depositor), 0.179 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.033	α = 90
b = 106.52	β = 90
c = 56.986	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-12-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-12-18
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

2VI8 | pdb_00002vi8

Crystal structure of S172AbsSHMT internal aldimine

Literature

Crystal Structure of S172Absshmt and its Complexes

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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