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- PDB-7byi: Structure of SHMT2 in complex with CBX -

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Basic information

Entry
Database: PDB / ID: 7byi
TitleStructure of SHMT2 in complex with CBX
Components(Serine hydroxymethyltransferase, ...) x 2
KeywordsTRANSFERASE / SHMT2 / CBX / STRUCTURAL PROTEIN
Function / homology
Function and homology information


BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / L-serine metabolic process / glycine metabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding ...BRISC complex / L-allo-threonine aldolase activity / regulation of mitochondrial translation / L-serine metabolic process / glycine metabolic process / L-serine biosynthetic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / Metabolism of folate and pterines / L-serine catabolic process / regulation of oxidative phosphorylation / tetrahydrofolate metabolic process / response to type I interferon / protein K63-linked deubiquitination / tetrahydrofolate interconversion / regulation of aerobic respiration / cobalt ion binding / mitochondrial nucleoid / RHOG GTPase cycle / folic acid metabolic process / Mitochondrial protein degradation / protein tetramerization / microtubule cytoskeleton / pyridoxal phosphate binding / one-carbon metabolic process / protein homotetramerization / mitochondrial inner membrane / mitochondrial matrix / chromatin binding / positive regulation of cell population proliferation / mitochondrion / zinc ion binding / extracellular exosome / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
CARBENOXOLONE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Serine hydroxymethyltransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsLi, L. / Chen, Y. / Lu, D. / Zhang, C. / Su, D.
CitationJournal: To Be Published
Title: Structure of SHMT2 with CBX
Authors: Li, L. / Su, D.
History
DepositionApr 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Jun 7, 2023Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase, mitochondrial
B: Serine hydroxymethyltransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1447
Polymers106,7062
Non-polymers1,4385
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-65 kcal/mol
Surface area33160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.620, 158.620, 209.427
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Serine hydroxymethyltransferase, ... , 2 types, 2 molecules AB

#1: Protein Serine hydroxymethyltransferase, mitochondrial / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 53480.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P34897, glycine hydroxymethyltransferase
#2: Protein Serine hydroxymethyltransferase, mitochondrial / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 53225.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT2 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P34897, glycine hydroxymethyltransferase

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Non-polymers , 4 types, 83 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CBO / CARBENOXOLONE


Mass: 570.757 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H50O7 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.49 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium dihydrogen phosphate pH 6.5, 16% PEG 2000,2.5mM Carbenoxolone Sodium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 38383 / % possible obs: 100 % / Redundancy: 21.2 % / CC1/2: 0.973 / Net I/σ(I): 18.25
Reflection shellResolution: 2.76→2.84 Å / Num. unique obs: 6297 / CC1/2: 0.884

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H3C

6h3c


Resolution: 2.76→34.5 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.874 / SU B: 36.987 / SU ML: 0.343 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.616 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.3108 2125 5.2 %RANDOM
Rwork0.2416 ---
obs0.2453 38383 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 203.12 Å2 / Biso mean: 67.654 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.54 Å20 Å2
2--1.07 Å2-0 Å2
3----3.48 Å2
Refinement stepCycle: final / Resolution: 2.76→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7187 0 99 78 7364
Biso mean--126.96 52.29 -
Num. residues----925
LS refinement shellResolution: 2.76→2.831 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 162 -
Rwork0.316 2787 -
all-2949 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.36080.12150.19120.26910.65081.7658-0.10050.0807-0.0531-0.1110.085-0.0097-0.31070.07750.01550.1714-0.06740.00860.1629-0.0290.011732.447-57.746.303
20.20.03880.17620.3659-0.04790.294-0.0492-0.0122-0.00160.0438-0.0198-0.01090.0497-0.20910.0690.1279-0.16320.06120.3613-0.11120.03935.028-73.796.321
300000000000000-00.0951000.095100.0951000
400000000000000-00.0951000.095100.0951000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 205
2X-RAY DIFFRACTION1A206 - 368
3X-RAY DIFFRACTION1A369 - 504
4X-RAY DIFFRACTION2B43 - 127
5X-RAY DIFFRACTION2B128 - 303
6X-RAY DIFFRACTION2B304 - 380
7X-RAY DIFFRACTION2B381 - 504

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