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- PDB-3ndn: Crystal structure of O-succinylhomoserine sulfhydrylase from Myco... -

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Basic information

Entry
Database: PDB / ID: 3ndn
TitleCrystal structure of O-succinylhomoserine sulfhydrylase from Mycobacterium tuberculosis covalently bound to pyridoxal-5-phosphate
ComponentsO-succinylhomoserine sulfhydrylase
KeywordsLYASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / mycobacterium / tuberculosis / PLP / Schiff base / transamination
Function / homology
Function and homology information


homocysteine biosynthetic process / carbon-sulfur lyase activity / cystathionine gamma-lyase activity / 'de novo' L-methionine biosynthetic process / cysteine biosynthetic process via cystathionine / transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
O-succinylhomoserine sulfhydrylase / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / 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 ...O-succinylhomoserine sulfhydrylase / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / 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
O-succinylhomoserine sulfhydrylase / O-succinylhomoserine sulfhydrylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJun 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-succinylhomoserine sulfhydrylase
B: O-succinylhomoserine sulfhydrylase
C: O-succinylhomoserine sulfhydrylase
D: O-succinylhomoserine sulfhydrylase


Theoretical massNumber of molelcules
Total (without water)178,5894
Polymers178,5894
Non-polymers00
Water18,8441046
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21910 Å2
ΔGint-111 kcal/mol
Surface area48750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.950, 129.560, 95.960
Angle α, β, γ (deg.)90.000, 115.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
O-succinylhomoserine sulfhydrylase


Mass: 44647.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: metZ, MT0402, Rv0391 / Production host: Escherichia coli (E. coli)
References: UniProt: P95199, UniProt: P9WGB5*PLUS, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1046 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 26.9 mg/mL protein against JCSG+ condition A2, 25% PEG 3000, 0.1 M citrate pH 5.5, crystal tracking ID 215797a2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 154137 / Num. obs: 153275 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 33.417 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.94.20.5292.5475631130499.6
1.9-1.950.492.9466441098399.1
1.95-2.010.3564.2451791067599.1
2.01-2.070.2585.2457871043799.8
2.07-2.140.2126.6440561010499.6
2.14-2.210.177.944050981899.8
2.21-2.290.1489.441396939199.2
2.29-2.390.12411.239908903299.1
2.39-2.490.10112.839362871799.8
2.49-2.620.08914.637200833999.8
2.62-2.760.07417.235050797099.7
2.76-2.930.06319.533093753099.7
2.93-3.130.05621.630884706199.7
3.13-3.380.0524.228458656099.8
3.38-3.70.04427.125964607899.6
3.7-4.140.0422923022549299.3
4.14-4.780.03930.620262483699.5
4.78-5.850.03631.418276411199.7
5.85-8.270.03231.814430318999.7
8.270.02733.57359164891.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.38 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.71 Å
Translation3 Å19.71 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1y4i

1y4i


Resolution: 1.85→19.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.824 / SU B: 7.846 / SU ML: 0.102 / SU R Cruickshank DPI: 0.133 / SU Rfree: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.223 7681 5 %RANDOM
Rwork0.187 ---
obs0.189 153169 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.07 Å2 / Biso mean: 39.709 Å2 / Biso min: 16.14 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å2-1.07 Å2
2--1.56 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12027 0 0 1046 13073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212394
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.96416901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.27151631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57222.967509
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.037151889
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2481597
X-RAY DIFFRACTIONr_chiral_restr0.090.21926
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219501
X-RAY DIFFRACTIONr_mcbond_it0.5251.57984
X-RAY DIFFRACTIONr_mcangle_it0.953212774
X-RAY DIFFRACTIONr_scbond_it1.51234410
X-RAY DIFFRACTIONr_scangle_it2.5294.54111
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 605 -
Rwork0.285 10673 -
all-11278 -
obs--99.63 %
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)
10.1209-0.0222-0.09350.41420.12350.18160.05640.04350.0099-0.0097-0.0664-0.0224-0.0267-0.06180.010.10120.0651-0.00030.13350.03630.096718.396515.011422.702
20.3202-0.0526-0.09340.21980.0130.3220.01360.0007-0.00040.072-0.0357-0.0535-0.0055-0.0270.02220.12480.008-0.02410.080.04440.116935.91847.423754.785
30.26160.0266-0.05460.09690.13060.2372-0.00120.0217-0.06970.0368-0.0108-0.04770.08140.02920.01190.09440.0683-0.00390.10260.07950.184155.9775-14.121538.5325
40.2295-0.1496-0.10540.15560.11410.17520.14130.15980.0456-0.0518-0.1328-0.08880.0395-0.0588-0.00850.16190.1140.03120.17090.09280.096934.4387-10.83217.886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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