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- PDB-3n0l: Crystal structure of serine hydroxymethyltransferase from Campylo... -

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Basic information

Entry
Database: PDB / ID: 3n0l
TitleCrystal structure of serine hydroxymethyltransferase from Campylobacter jejuni
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / Campylobacter / alpha beta class / 3-layer(aba) sandwich / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate 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) ...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
Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Hasseman, J. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of serine hydroxymethyltransferase from Campylobacter jejuni
Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Hasseman, J. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Database references / Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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)94,87617
Polymers93,4352
Non-polymers1,44115
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-284 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.558, 108.319, 126.072
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine hydroxymethyltransferase / Serine methylase / SHMT


Mass: 46717.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: glyA, Cj0402 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: P24531, glycine hydroxymethyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 1500, 200mM NH4 Sulfate, 100mM Bis-Tris, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2010 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 75163 / Num. obs: 74111 / % possible obs: 98.6 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2.2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.076 / Χ2: 1.002 / Net I/σ(I): 10.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6547 / Χ2: 0.98 / % possible all: 88.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→31.3 Å / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.883 / SU ML: 0.21 / σ(F): 1.44 / σ(I): 2.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3739 5.05 %random
Rwork0.16 ---
obs0.162 74028 98.32 %-
all-75293 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.77 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 104.37 Å2 / Biso mean: 29.072 Å2 / Biso min: 7.84 Å2
Baniso -1Baniso -2Baniso -3
1--6.296 Å20 Å20 Å2
2--3.612 Å2-0 Å2
3---2.683 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6245 0 75 497 6817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076517
X-RAY DIFFRACTIONf_angle_d1.068809
X-RAY DIFFRACTIONf_chiral_restr0.073963
X-RAY DIFFRACTIONf_plane_restr0.0041141
X-RAY DIFFRACTIONf_dihedral_angle_d12.1452461
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.8620.2853160.2560166332601685
1.862-1.9370.2473920.19769297321692998
1.937-2.0250.2223380.172707974177079100
2.025-2.1320.2183890.156705574447055100
2.132-2.2650.1883760.144710174777101100
2.265-2.440.1894220.153708375057083100
2.44-2.6860.2033820.154712275047122100
2.686-3.0740.1713770.148718775647187100
3.074-3.8720.1823690.142722575947225100
3.872-31.3350.193780.163749278707492100
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)
10.71080.2549-0.31480.3087-0.17660.175-0.10310.068-0.1805-0.0778-0.0056-0.09490.08410.02020.06930.1617-0.00530.0070.1547-0.05910.16875.0396-30.5358-43.6866
20.81010.79530.00671.24910.2710.49050.1594-0.1261-0.08510.1549-0.1391-0.01610.0902-0.0116-0.00970.10060.00080.00440.16840.01970.150917.7313-19.7276-24.0932
31.42260.7374-0.15340.7197-0.05940.7220.0391-0.04380.09040.0548-0.0304-0.042-0.06730.0288-0.0080.07990.02090.00450.1177-0.00120.152224.8097-12.252-32.4306
41.20150.0912-0.16091.3054-0.00770.97790.00120.2712-0.0442-0.3032-0.08540.0082-0.0207-0.00920.05230.1850.03290.0160.2026-0.08480.130719.3152-16.9402-57.9656
51.15340.1955-0.68040.08240.04880.9477-0.0504-0.0202-0.3262-0.0531-0.0112-0.15560.2004-0.01360.05310.1568-0.0001-0.00130.08530.00240.23326.2073-36.7866-29.885
60.3945-0.0269-0.20790.91120.17050.29680.0270.02620.0591-0.11280.003-0.0924-0.08290.1146-0.03490.111-0.011-0.00580.142-0.0250.138-2.9784-13.3513-34.0682
71.1809-0.08-0.21111.0789-0.22120.88270.0149-0.13970.1190.11020.00360.0005-0.1057-0.0213-0.00770.0867-0.0054-0.01670.0956-0.03770.0865-8.8011-13.1058-22.1836
81.26040.60470.17071.8975-0.40580.76940.1182-0.3295-0.29150.4156-0.1478-0.1760.0062-0.0861-0.03020.1937-0.0623-0.05820.1710.0940.1594-6.357-35.9463-8.8269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:50)A1 - 50
2X-RAY DIFFRACTION2(chain A and resid 51:133)A51 - 133
3X-RAY DIFFRACTION3(chain A and resid 134:276)A134 - 276
4X-RAY DIFFRACTION4(chain A and resid 277:414)A277 - 414
5X-RAY DIFFRACTION5(chain B and resid 1:51)B1 - 51
6X-RAY DIFFRACTION6(chain B and resid 52:133)B52 - 133
7X-RAY DIFFRACTION7(chain B and resid 134:276)B134 - 276
8X-RAY DIFFRACTION8(chain B and resid 277:414)B277 - 414

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