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- PDB-2g4r: anomalous substructure of MogA -

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Basic information

Entry
Database: PDB / ID: 2g4r
Titleanomalous substructure of MogA
Componentsmolybdopterin biosynthesis Mog protein
KeywordsBIOSYNTHETIC PROTEIN / anomalous substructure of MogA
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process
Similarity search - Function
: / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Molybdopterin biosynthesis Mog protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.92 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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 biosynthesis Mog protein
B: molybdopterin biosynthesis Mog protein
C: molybdopterin biosynthesis Mog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7675
Polymers48,6103
Non-polymers1582
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.590, 97.840, 57.710
Angle α, β, γ (deg.)90.00, 105.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein molybdopterin biosynthesis Mog protein / mogA


Mass: 16203.224 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mog / Production host: Escherichia coli (E. coli) / References: GenBank: 13880438, UniProt: O53877*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 25758 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.92→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.973 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24139 483 1.9 %RANDOM
Rwork0.17878 ---
obs0.18004 25275 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.34 Å2
2--0.5 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.92→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 9 151 3316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223232
X-RAY DIFFRACTIONr_bond_other_d0.0020.023077
X-RAY DIFFRACTIONr_angle_refined_deg1.761.974432
X-RAY DIFFRACTIONr_angle_other_deg0.93937105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0565448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65623.839112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39215456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1361523
X-RAY DIFFRACTIONr_chiral_restr0.1080.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023685
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02583
X-RAY DIFFRACTIONr_nbd_refined0.2220.2731
X-RAY DIFFRACTIONr_nbd_other0.1920.23120
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21613
X-RAY DIFFRACTIONr_nbtor_other0.0860.21974
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2149
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0590.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.214
X-RAY DIFFRACTIONr_mcbond_it1.5281.52823
X-RAY DIFFRACTIONr_mcbond_other0.2631.5934
X-RAY DIFFRACTIONr_mcangle_it1.9982.53566
X-RAY DIFFRACTIONr_scbond_it4.57551103
X-RAY DIFFRACTIONr_scangle_it6.35210863
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 33 -
Rwork0.285 1832 -
obs--97.49 %
Refinement TLS params.Method: refined / Origin x: 3.9453 Å / Origin y: 3.7901 Å / Origin z: 35.1939 Å
111213212223313233
T-0.0113 Å20.0167 Å2-0.0161 Å2-0.0144 Å20.0026 Å2--0.0104 Å2
L0.1586 °20.0979 °2-0.093 °2-0.1344 °20.0995 °2--0.3875 °2
S0.004 Å °-0.011 Å °0.0125 Å °-0.0332 Å °-0.0075 Å °-0.019 Å °-0.0579 Å °-0.0009 Å °0.0035 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1553 - 155
2X-RAY DIFFRACTION1BB4 - 1544 - 154
3X-RAY DIFFRACTION1CC4 - 1534 - 153

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