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- PDB-1mkz: Crystal structure of MoaB protein at 1.6 A resolution. -

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Basic information

Entry
Database: PDB / ID: 1mkz
TitleCrystal structure of MoaB protein at 1.6 A resolution.
ComponentsMolybdenum cofactor biosynthesis protein B
KeywordsBIOSYNTHETIC PROTEIN / MAD / Weak anomalous signal / Molybdopterin synthesis / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process / protein hexamerization / GTP binding / identical protein binding / cytosol
Similarity search - Function
Molybdenum cofactor biosynthesis protein B, proteobacteria / Molybdenum cofactor biosynthesis protein MoaB / Molybdenum cofactor biosynthesis proteins signature 1. / Molybdenum cofactor biosynthesis, conserved site / 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 ...Molybdenum cofactor biosynthesis protein B, proteobacteria / Molybdenum cofactor biosynthesis protein MoaB / Molybdenum cofactor biosynthesis proteins signature 1. / Molybdenum cofactor biosynthesis, conserved site / 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
ACETIC ACID / Molybdenum cofactor biosynthesis protein B / Molybdenum cofactor biosynthesis protein B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsSanishvili, R. / Skarina, T. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The crystal structure of Escherichia coli MoaB suggests a probable role in molybdenum cofactor synthesis.
Authors: Sanishvili, R. / Beasley, S. / Skarina, T. / Glesne, D. / Joachimiak, A. / Edwards, A. / Savchenko, A.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / 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_database_related.db_name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE F134L is either a gene sequencing error or else there was a mutation introduced during PCR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein B
B: Molybdenum cofactor biosynthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,73012
Polymers37,8782
Non-polymers85310
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.169, 69.169, 126.184
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsBiological assembly could be symmetry generated trimer or hexamer

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Components

#1: Protein Molybdenum cofactor biosynthesis protein B


Mass: 18938.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MoaB / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30746, UniProt: P0AEZ9*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mammonium sulfate1reservoir
220 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
DetectorType: CUSTOM-MADE / Detector: CCD
RadiationMonochromator: sagitally focusing double crystal monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→129.1 Å / Num. obs: 42215
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 129.1 Å / Num. obs: 55534 / % possible obs: 99.4 % / Num. measured all: 311387 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
CNSrefinement
WARPmodel building
d*TREKdata scaling
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
ARP/wARPmodel building
RefinementResolution: 1.6→129.1 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.703 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21871 2248 5.1 %RANDOM
Rwork0.18284 ---
obs0.18461 42215 94.81 %-
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: 14.768 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→129.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 35 247 2961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212762
X-RAY DIFFRACTIONr_bond_other_d0.0010.022551
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.9553754
X-RAY DIFFRACTIONr_angle_other_deg0.85635920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023019
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02537
X-RAY DIFFRACTIONr_nbd_refined0.240.3539
X-RAY DIFFRACTIONr_nbd_other0.2660.32945
X-RAY DIFFRACTIONr_nbtor_other0.0910.51627
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.5306
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.333
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3290.3109
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.522
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8861.51719
X-RAY DIFFRACTIONr_mcangle_it1.48722795
X-RAY DIFFRACTIONr_scbond_it2.59531043
X-RAY DIFFRACTIONr_scangle_it3.6414.5959
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 176
Rwork0.206 2876
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)
11.2326-0.23930.13051.25640.06322.5274-0.0314-0.204-0.07310.2121-0.00580.11230.0745-0.05320.03720.0799-0.00470.04550.0994-0.00110.115417.855314.023148.2434
20.9430.2865-0.46491.2244-0.03712.4576-0.03960.07910.0268-0.0657-0.00120.10790.0413-0.17450.04080.0136-0.011-0.02940.0261-0.00140.100118.176612.995214.6819
30.3565-0.0275-0.18160.34840.10042.0293-0.0206-0.0496-0.02840.0433-0.00460.10930.1077-0.1010.02520.1456-0.0161-0.00080.1640.02250.257117.734612.363328.7149
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1723 - 172
2X-RAY DIFFRACTION2BB3 - 1722 - 172
3X-RAY DIFFRACTION3A - BM - N1202 - 13361 - 133
Refinement
*PLUS
Lowest resolution: 129.1 Å / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_d0.020.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.8851.955
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg6.2855
X-RAY DIFFRACTIONr_plane_restr0.0070.02
X-RAY DIFFRACTIONr_chiral_restr0.2
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.64 Å / Num. reflection Rwork: 2867

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