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- PDB-4bhd: Methanococcus jannaschii serine hydroxymethyl-transferase, apo form -

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Basic information

Entry
Database: PDB / ID: 4bhd
TitleMethanococcus jannaschii serine hydroxymethyl-transferase, apo form
ComponentsSERINE HYDROXYMETHYLTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases / L-allo-threonine aldolase / L-allo-threonine aldolase activity / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process ...Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases / L-allo-threonine aldolase / L-allo-threonine aldolase activity / serine binding / L-serine catabolic process / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid metabolic process / pyridoxal phosphate binding / one-carbon metabolic process / zinc ion binding / cytoplasm
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesMETHANOCALDOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsSaccoccia, F. / Angelucci, F. / Ilari, A.
CitationJournal: Proteins / Year: 2014
Title: The Crystal Structure of Archaeal Serine Hydroxymethyltransferase Reveals Idiosyncratic Features Likely Required to Withstand High Temperatures.
Authors: Angelucci, F. / Morea, V. / Angelaccio, S. / Saccoccia, F. / Contestabile, R. / Ilari, A.
History
DepositionApr 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE HYDROXYMETHYLTRANSFERASE
B: SERINE HYDROXYMETHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1363
Polymers96,0412
Non-polymers951
Water28816
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-64.1 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.594, 110.158, 110.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRTYRTYRAA280 - 429279 - 428
21TYRTYRTYRTYRBB280 - 429279 - 428
12ASPASPGLUGLUAA5 - 404 - 39
22ASPASPGLUGLUBB5 - 404 - 39

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Components

#1: Protein SERINE HYDROXYMETHYLTRANSFERASE / SHMT / SERINE METHYLASE / L-ALLO-THREONINE ALDOLASE


Mass: 48020.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174 (DE3)
References: UniProt: Q58992, glycine hydroxymethyltransferase, L-allo-threonine aldolase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.22 % / Description: NONE
Crystal growpH: 5 / Details: NAH2PO4/K2HPO4 1.8 M, PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 25528 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.93
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.53 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KL2

1kl2


Resolution: 2.83→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.865 / SU B: 40.373 / SU ML: 0.356 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29768 1293 5.1 %RANDOM
Rwork0.24209 ---
obs0.24474 24195 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.509 Å2
Baniso -1Baniso -2Baniso -3
1--2.94 Å20 Å20 Å2
2---1.51 Å20 Å2
3---4.45 Å2
Refinement stepCycle: LAST / Resolution: 2.83→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6391 0 5 16 6412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226535
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9921.9568815
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9845804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01325.194310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.631151159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9861521
X-RAY DIFFRACTIONr_chiral_restr0.0720.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214947
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2231.54028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.41726466
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.42132507
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.7534.52349
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
744medium positional0.210.5
782loose positional0.525
744medium thermal0.52
782loose thermal0.6310
LS refinement shellResolution: 2.825→2.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 87 -
Rwork0.33 1601 -
obs--88.94 %
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)
12.68460.2857-0.69892.5139-0.88831.53150.15630.4102-0.0701-0.4838-0.0692-0.448-0.08680.0788-0.08710.17120.03520.1070.1589-0.03530.173128.7098-14.3588-14.1435
23.42681.1516-0.62825.0652-1.071.350.19030.40220.2079-0.33310.01420.1583-0.1605-0.1995-0.20450.09720.07240.04650.1740.02710.056215.0328-10.8401-7.3858
32.5727-0.80840.21382.71930.87734.43740.50390.7169-0.5511-0.9793-0.5820.84740.062-1.29660.07810.57430.1381-0.11840.7318-0.17840.62831.699-20.3392-33.7618
44.4893-3.9367-2.09567.63642.52493.71130.4860.47470.0779-0.7879-0.3001-0.86170.0322-0.0102-0.18590.2970.06920.23430.20470.00890.300752.74-24.0941-31.0756
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 118
2X-RAY DIFFRACTION2A119 - 429
3X-RAY DIFFRACTION3B2 - 265
4X-RAY DIFFRACTION4B266 - 429

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