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- PDB-2wp4: crystal structure of Rv3119 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 2wp4
Titlecrystal structure of Rv3119 from Mycobacterium tuberculosis
ComponentsMOLYBDOPTERIN-CONVERTING FACTOR SUBUNIT 2 1
KeywordsTRANSFERASE
Function / homology
Function and homology information


molybdopterin synthase activity / molybdopterin synthase / Mo-molybdopterin cofactor biosynthetic process / cytosol
Similarity search - Function
Molybdopterin biosynthesis MoaE subunit / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Aldehyde Oxidoreductase; domain 3 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Molybdopterin synthase catalytic subunit 1 / Molybdopterin synthase catalytic subunit 1
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsCho, H.J. / Kang, B.S.
CitationJournal: To be Published
Title: Crystal Structure of Rv3119 from Mycobacterium Tuberculosis
Authors: Cho, H.J. / Kang, B.S.
History
DepositionAug 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: MOLYBDOPTERIN-CONVERTING FACTOR SUBUNIT 2 1
B: MOLYBDOPTERIN-CONVERTING FACTOR SUBUNIT 2 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0084
Polymers31,8762
Non-polymers1322
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-16.4 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.464, 64.353, 91.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MOLYBDOPTERIN-CONVERTING FACTOR SUBUNIT 2 1 / MOLYBDOPTERIN SYNTHASE SUBUNIT 2 1 / MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN E 1 / MOLYBDOPTERIN- ...MOLYBDOPTERIN SYNTHASE SUBUNIT 2 1 / MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN E 1 / MOLYBDOPTERIN-CONVERTING FACTOR LARGE SUBUNIT 1 / MPT SYNTHASE SUBUNIT 2 1


Mass: 15938.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O05795, UniProt: P9WJR3*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.72 Å3/Da / Density % sol: 54.8 % / Description: NONE
Crystal growDetails: 30% MPD, 0.1 M ACETATE PH 4.6, 0.02 M CALCIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: May 31, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13457 / % possible obs: 99.9 % / Observed criterion σ(I): 2.5 / Redundancy: 7.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 37.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q5W

2q5w


Resolution: 2.49→44.82 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.935 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 47-53 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.24694 663 4.9 %RANDOM
Rwork0.20014 ---
obs0.20236 12753 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.616 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--0.95 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.49→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 7 38 1974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221968
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.9672668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0555249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06723.25686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99415319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3991518
X-RAY DIFFRACTIONr_chiral_restr0.0730.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211489
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4011.51256
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.77722020
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2313712
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1334.5648
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.494→2.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 49 -
Rwork0.238 910 -
obs--98.76 %
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)
12.2671-1.1976-0.71653.39351.65514.7799-0.1819-0.12910.04380.08070.1011-0.03450.0763-0.18820.08080.1778-0.0137-0.02040.04580.0250.11355.9796.4437.377
23.781-1.2862-1.48672.64161.08174.21890.01860.1119-0.0233-0.14790.0275-0.00550.21190.0145-0.04610.2616-0.0078-0.04030.00980.0170.097817.3194.387-12.762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 137
2X-RAY DIFFRACTION2B2 - 134

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