9XBR | pdb_00009xbr

Crystal structure of OsSHMT1-WT

PDB DOI: https://doi.org/10.2210/pdb9XBR/pdb

Classification: PLANT PROTEIN
Organism(s): Oryza sativa
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2025-10-24 Released: 2026-10-28
Deposition Author(s): Li, Z.R.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.260 (Depositor), 0.260 (DCC)
R-Value Work:
0.212 (Depositor), 0.212 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9XBR

This is version 1.0 of the entry. See complete history.

Literature

Structure of SHMT at 3.5

Li, Z.R.

To be published.

Macromolecule Content

Total Structure Weight: 112.98 kDa
Atom Count: 7,314
Modeled Residue Count: 948
Deposited Residue Count: 1,026
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SHMT protein	A, B	513	Oryza sativa	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.260 (Depositor), 0.260 (DCC)
R-Value Work: 0.212 (Depositor), 0.212 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.371	α = 90
b = 167.371	β = 90
c = 74.543	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32172433

Revision History (Full details and data files)

Version 1.0: 2026-10-28
Type: Initial release