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- PDB-3qi6: Crystal Structure of Cystathionine gamma-synthase MetB (Cgs) from... -

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Basic information

Entry
Database: PDB / ID: 3qi6
TitleCrystal Structure of Cystathionine gamma-synthase MetB (Cgs) from Mycobacterium ulcerans Agy99
ComponentsCystathionine gamma-synthase MetB (Cgs)
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / CGS_like / AAT_I superfamily / LLP / PLP
Function / homology
Function and homology information


transsulfuration / methionine biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / 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 ...Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / 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
Cystathionine gamma-synthase MetB (Cgs)
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
#1: Journal: 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
DepositionJan 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Database references / Refinement description
Revision 1.3Mar 28, 2012Group: Database references
Revision 1.4Apr 22, 2015Group: Database references
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software
Revision 1.6Sep 13, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Dec 6, 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: Cystathionine gamma-synthase MetB (Cgs)
B: Cystathionine gamma-synthase MetB (Cgs)
C: Cystathionine gamma-synthase MetB (Cgs)
D: Cystathionine gamma-synthase MetB (Cgs)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,91513
Polymers165,1654
Non-polymers7509
Water25,9421440
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20840 Å2
ΔGint-198 kcal/mol
Surface area41840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.956, 106.924, 100.307
Angle α, β, γ (deg.)90.000, 113.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cystathionine gamma-synthase MetB (Cgs) / O-succinylhomoserine (thiol)-lyase


Mass: 41291.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (bacteria) / Strain: Agy99 / Gene: metB, MUL_0201 / Production host: Escherichia coli (E. coli) / References: UniProt: A0PKT3, cystathionine gamma-synthase

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Non-polymers , 5 types, 1449 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1440 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25.5% PEG4000, 15% glycerol, 170 mM ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 18, 2010 / Details: Varimax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.91→44.468 Å / Num. obs: 119042 / % possible obs: 98.1 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.103 / Χ2: 0.958 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.91-1.982.80.263108710.661189.4
1.98-2.063.50.236115500.894195.8
2.06-2.1540.209117751.012197.7
2.15-2.264.60.19119281.049198.4
2.26-2.415.30.173120210.965199.4
2.41-2.596.10.157121261.0071100
2.59-2.856.30.129121291.0061100
2.85-3.276.40.104121540.9721100
3.27-4.116.50.082121690.9441100
4.11-506.50.063123190.886199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.92 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.52 Å
Translation2.5 Å44.52 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NNP

3nnp
PDB Unreleased entry


Resolution: 1.91→44.468 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2492 / WRfactor Rwork: 0.2094 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8016 / SU B: 7.373 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1741 / SU Rfree: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 5969 5 %RANDOM
Rwork0.1998 ---
obs0.2019 118776 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.6 Å2 / Biso mean: 16.2273 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å2-0.77 Å2
2--1.47 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.91→44.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10835 0 42 1440 12317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.02211280
X-RAY DIFFRACTIONr_bond_other_d0.0010.027213
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.97515452
X-RAY DIFFRACTIONr_angle_other_deg2.244317652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8451544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09123.56441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.394151621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5511579
X-RAY DIFFRACTIONr_chiral_restr0.1340.21804
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02112967
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022239
X-RAY DIFFRACTIONr_mcbond_it1.2131.57472
X-RAY DIFFRACTIONr_mcbond_other0.2461.53068
X-RAY DIFFRACTIONr_mcangle_it1.765211892
X-RAY DIFFRACTIONr_scbond_it3.04733808
X-RAY DIFFRACTIONr_scangle_it4.2754.53530
LS refinement shellResolution: 1.909→1.958 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 389 -
Rwork0.229 7444 -
all-7833 -
obs--87.99 %
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)
10.3485-0.0343-0.0350.0689-0.02920.25880.00230.03230.00860.00070.0118-0.01270.00010.0306-0.0140.0205-0.0035-0.00090.0136-0.00530.00624.5557-23.5075-37.211
20.3601-0.04180.0120.11230.0370.28230.00230.0339-0.00080.00630.01150.0105-0.0127-0.0338-0.01370.0208-0.003-0.00490.01340.00740.0113-28.9811-20.995-36.9447
30.29170.01090.0240.108-0.03010.3126-0.0035-0.06240.002-0.00280.0205-0.0133-0.0020.0396-0.01690.00770.0047-0.00250.0297-0.00870.00444.5102-21.0862-0.285
40.24970.0236-0.02250.08270.04770.35660.002-0.0527-0.01480.01010.0110.01380.0251-0.0216-0.0130.01540.0048-0.00090.02020.00890.0096-29.0379-23.6274-0.1439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 388
2X-RAY DIFFRACTION2B10 - 388
3X-RAY DIFFRACTION3C12 - 388
4X-RAY DIFFRACTION4D11 - 387

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