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- PDB-2ghr: Crystal structure of homoserine o-succinyltransferase (NP_981826.... -

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Basic information

Entry
Database: PDB / ID: 2ghr
TitleCrystal structure of homoserine o-succinyltransferase (NP_981826.1) from Bacillus cereus ATCC 10987 at 2.40 A resolution
ComponentsHomoserine O-succinyltransferase
KeywordsTRANSFERASE / NP_981826.1 / HOMOSERINE O-SUCCINYLTRANSFERASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


homoserine O-succinyltransferase activity / L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine / homoserine O-acetyltransferase / homoserine O-acetyltransferase activity / cytoplasm
Similarity search - Function
Homoserine O-succinyltransferase MetA / MetA family / Homoserine O-succinyltransferase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Homoserine O-acetyltransferase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution
Authors: Zubieta, C. / Krishna, S.S. / McMullan, D. / Miller, M.D. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Chiu, H.J. / Clayton, T. / Deller, M. / ...Authors: Zubieta, C. / Krishna, S.S. / McMullan, D. / Miller, M.D. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Chiu, H.J. / Clayton, T. / Deller, M. / Didonato, M. / Duan, L. / Elsliger, M.A. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Han, G.W. / Haugen, J. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Kumar, A. / Marciano, D. / Morse, A.T. / Nigoghossian, E. / Oommachen, S. / Reyes, R. / Rife, C.L. / Bedem, H.V. / Weekes, D. / White, A. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionMar 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homoserine O-succinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8252
Polymers35,7291
Non-polymers961
Water1,40578
1
A: Homoserine O-succinyltransferase
hetero molecules

A: Homoserine O-succinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6494
Polymers71,4572
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+7/41
Buried area4220 Å2
ΔGint-41 kcal/mol
Surface area24830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.890, 95.890, 75.403
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Homoserine O-succinyltransferase / Homoserine O- transsuccinylase / HTS


Mass: 35728.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: metA / Production host: Escherichia coli (E. coli)
References: UniProt: Q72X44, homoserine O-succinyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8
Details: 1.6M (NH4)2SO4, 0.1M TRIS pH 8.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.918381, 0.979094,0.978532
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2006
Details: 1m long Rh coated bent cylindrical mirror for horizontal and vertical focussing
RadiationMonochromator: Double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9183811
20.9790941
30.9785321
ReflectionResolution: 2.4→29.64 Å / Num. obs: 14274 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.4-2.461006.80.5921.310380.592
2.46-2.531006.80.5321.410010.532
2.53-2.61006.80.5231.59890.523
2.6-2.681006.90.4311.89420.431
2.68-2.771006.90.362.19240.36
2.77-2.871006.80.3212.48900.321
2.87-2.981006.80.272.88890.27
2.98-3.11006.80.1874.18290.187
3.1-3.241006.80.1554.98060.155
3.24-3.391006.80.1226.37780.122
3.39-3.581006.70.0967.77290.096
3.58-3.7999.35.70.1353.76950.135
3.79-4.0699.86.50.0759.16620.075
4.06-4.381006.50.05412.86210.054
4.38-4.899.96.40.04713.85680.047
4.8-5.3799.86.20.051135260.051
5.37-6.2995.50.0688.94640.068
6.2-7.5999.76.50.0659.24050.065
7.59-10.731006.30.03516.43280.035
10.73-29.6494.75.50.03517.31900.035

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.028 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.255
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE MAIN CHAIN AT PRO45 MAY NOT BE RELIABLE. 3. DUE TO WEAK DENSITY DUE TO A STRONG ICE RING, 263 REFLECTIONS BETWEEN 3.63-3.71 ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE MAIN CHAIN AT PRO45 MAY NOT BE RELIABLE. 3. DUE TO WEAK DENSITY DUE TO A STRONG ICE RING, 263 REFLECTIONS BETWEEN 3.63-3.71 ANGSTROMS WERE OMITTED FROM THE FINAL REFINEMENT. 4. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25 699 5 %RANDOM
Rwork0.188 ---
all0.191 ---
obs0.19144 13291 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.813 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 5 78 2293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222265
X-RAY DIFFRACTIONr_bond_other_d0.0010.021990
X-RAY DIFFRACTIONr_angle_refined_deg0.7421.9453060
X-RAY DIFFRACTIONr_angle_other_deg0.51334631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3775267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.1424.426122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18315400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5661513
X-RAY DIFFRACTIONr_chiral_restr0.0490.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022511
X-RAY DIFFRACTIONr_gen_planes_other00.02470
X-RAY DIFFRACTIONr_nbd_refined0.2040.2415
X-RAY DIFFRACTIONr_nbd_other0.1950.21959
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21079
X-RAY DIFFRACTIONr_nbtor_other0.0860.21251
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.211
X-RAY DIFFRACTIONr_mcbond_it1.63231368
X-RAY DIFFRACTIONr_mcbond_other0.3583546
X-RAY DIFFRACTIONr_mcangle_it2.59352148
X-RAY DIFFRACTIONr_scbond_it4.57481013
X-RAY DIFFRACTIONr_scangle_it6.42111912
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 47 -
Rwork0.229 985 -
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)
128.071-10.12921.78849.8223-5.027112.3047-0.6366-0.55270.51240.15460.1609-0.83330.74731.27670.47570.31710.01010.01750.431-0.08240.237348.66325.02177.756
22.4284-0.6969-0.718712.9902-0.97410.32160.1582-0.8649-0.0121.0715-0.0059-0.8659-1.0131.6445-0.15240.0899-0.1605-0.10570.6033-0.05170.070237.5238.6557.645
33.81452.9284-4.96133.2634-0.509317.1759-0.18510.25490.95730.34990.15470.6561-0.825-1.63540.03040.21860.0933-0.0540.16410.01190.252613.19338.30351.029
42.281.8544-0.16693.8280.78657.4583-0.0397-0.16360.10170.0110.17560.0731-0.7372-0.2484-0.13590.24430.0128-0.01680.085-0.04060.211121.69339.75652.849
53.72871.80020.46592.15080.51612.9539-0.190.29860.2735-0.28080.18210.0267-0.36910.1150.00790.16840.0097-0.07140.08530.04820.038417.54532.30239.337
62.6952-0.12410.17311.48630.64883.35150.01770.0499-0.40630.04490.0034-0.09690.44990.1019-0.02110.20110.0456-0.06180.08680.05120.08916.90416.15450.441
75.5384-1.34050.34771.01780.70114.1737-0.0308-0.17650.19270.1430.0484-0.20980.45850.0927-0.01760.15980.0265-0.03430.0624-0.01450.170116.79726.43551.499
823.3415-4.432610.36751.9991-5.347616.18050.0289-0.43350.054-0.03220.0055-0.095-0.4081-1.1725-0.03440.07320.0592-0.06420.2463-0.0452-0.0003-4.26128.62555.129
93.6374-0.33930.40960.92980.23192.8970.0415-0.6905-0.18560.2434-0.09140.04790.1712-0.26740.050.16510.0227-0.06180.13570.04540.015311.4523.67861.258
1023.517114.904110.905830.4796-25.19454.0625-1.771-1.1767-1.7869-0.63990.874-2.08691.62023.49940.8969-0.01190.1317-0.04550.1634-0.06560.303437.65431.19351.529
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
1117 - 2718 - 28
2228 - 3729 - 38
3338 - 5339 - 54
4454 - 8755 - 88
5588 - 16089 - 161
66161 - 225162 - 226
77226 - 242227 - 243
88243 - 256244 - 257
99257 - 292258 - 293
1010293 - 297294 - 298

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