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

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Basic information

Entry
Database: PDB / ID: 3qhx
TitleCrystal Structure of Cystathionine gamma-synthase MetB (Cgs) from Mycobacterium ulcerans Agy99 bound to HEPES
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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)166,09513
Polymers165,1654
Non-polymers9309
Water26,7881487
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20940 Å2
ΔGint-200 kcal/mol
Surface area43050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.963, 106.326, 100.548
Angle α, β, γ (deg.)90.00, 113.72, 90.00
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, 1496 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1487 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
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: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2010
RadiationMonochromator: Asymmetric cut single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→29.231 Å / Num. all: 186847 / Num. obs: 182652 / % possible obs: 98 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.65-1.713.80.443196.5
1.71-1.783.80.362196.9
1.78-1.863.80.282197.1
1.86-1.963.80.222197.6
1.96-2.083.80.163197.9
2.08-2.243.80.126198.2
2.24-2.463.80.105198.5
2.46-2.823.80.085198.9
2.82-3.553.80.061199.2
3.55-303.80.036199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QI6

3qi6


Resolution: 1.65→29.231 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.168 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0809 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18077 9180 5 %RANDOM
Rwork0.14839 ---
obs0.15002 173473 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.438 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å2-0.13 Å2
2--0.78 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10936 0 52 1487 12475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.02211489
X-RAY DIFFRACTIONr_bond_other_d0.0010.027404
X-RAY DIFFRACTIONr_angle_refined_deg2.1571.97615755
X-RAY DIFFRACTIONr_angle_other_deg1.171318135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44551582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81823.567457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.352151682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.021581
X-RAY DIFFRACTIONr_chiral_restr0.1470.21827
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02113227
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022294
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_it1.351.57554
X-RAY DIFFRACTIONr_mcbond_other0.4761.53102
X-RAY DIFFRACTIONr_mcangle_it2.159212058
X-RAY DIFFRACTIONr_scbond_it3.1633935
X-RAY DIFFRACTIONr_scangle_it4.9714.53655
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 629 -
Rwork0.215 12340 -
obs--94.51 %
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)
10.1842-0.0309-0.03410.01640.04150.1820.00550.02190.0209-0.00020.00710.0026-0.01340.0152-0.01260.0322-0.00670.0030.03080.00330.03460.4284-17.0842-39.3553
20.1905-0.05910.0950.3023-0.17310.48810.00190.0121-0.03710.01750.0175-0.02990.0720.0636-0.01940.02460.01510.0010.0253-0.01890.043514.2415-37.6795-33.0681
30.2175-0.03750.02190.0165-0.04070.16770.00510.0255-0.02370.00010.0045-0.00010.009-0.0179-0.00950.0351-0.0048-0.00370.0307-0.00490.0334-23.7957-27.0736-39.9636
40.1937-0.0715-0.03970.43270.03320.3031-0.00740.01880.03270.02510.02090.0213-0.047-0.032-0.01350.02630.0104-0.00140.02460.01860.0421-38.3053-7.5839-31.5455
50.17590.04090.02620.01510.02330.20690.005-0.0212-0.0136-0.00090.00570.00280.00960.0149-0.01070.02910.0049-0.00380.03540.00250.03040.5244-26.62971.7775
60.22530.1381-0.06320.5183-0.16080.3677-0.0149-0.01930.0442-0.01480.0313-0.0146-0.03850.0376-0.01650.017-0.0081-0.00470.027-0.0220.041314.7334-6.4779-5.4303
70.19780.0104-0.03170.014-0.04240.18790.0052-0.03030.0225-0.00350.0071-0.0043-0.0107-0.008-0.01230.03150.00450.00370.0334-0.00330.0315-23.9276-16.88333.0416
80.17070.0433-0.01570.31150.07110.4227-0.0153-0.0081-0.0339-0.00770.02650.02920.0752-0.0252-0.01120.028-0.0055-0.00010.020.01660.0462-36.464-35.3105-6.0865
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 262
2X-RAY DIFFRACTION2A263 - 388
3X-RAY DIFFRACTION3B12 - 255
4X-RAY DIFFRACTION4B256 - 388
5X-RAY DIFFRACTION5C12 - 262
6X-RAY DIFFRACTION6C263 - 388
7X-RAY DIFFRACTION7D12 - 245
8X-RAY DIFFRACTION8D246 - 388

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