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- PDB-3k6a: Crystal structure of molybdenum cofactor biosynthesis protein mog... -

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Basic information

Entry
Database: PDB / ID: 3k6a
TitleCrystal structure of molybdenum cofactor biosynthesis protein mog from shewanella oneidensis
ComponentsMolybdenum cofactor biosynthesis protein Mog
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN MOG / PSI / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process / metal ion binding
Similarity search - Function
: / 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
Molybdenum cofactor biosynthesis protein MogA
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
AuthorsChang, C. / Bigelow, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Molybdenum Cofactor Biosynthesis Protein Mog from Shewanella Oneidensis
Authors: Chang, C. / Bigelow, L. / Joachimiak, A.
History
DepositionOct 8, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionOct 20, 2009ID: 2FUW
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 26, 2012Group: Structure summary
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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.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_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

Downloads & links

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Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein Mog
B: Molybdenum cofactor biosynthesis protein Mog
C: Molybdenum cofactor biosynthesis protein Mog
D: Molybdenum cofactor biosynthesis protein Mog
E: Molybdenum cofactor biosynthesis protein Mog
F: Molybdenum cofactor biosynthesis protein Mog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4759
Polymers119,4066
Non-polymers693
Water16,087893
1
A: Molybdenum cofactor biosynthesis protein Mog
C: Molybdenum cofactor biosynthesis protein Mog
E: Molybdenum cofactor biosynthesis protein Mog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7495
Polymers59,7033
Non-polymers462
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-56 kcal/mol
Surface area21950 Å2
MethodPISA
2
B: Molybdenum cofactor biosynthesis protein Mog
D: Molybdenum cofactor biosynthesis protein Mog
F: Molybdenum cofactor biosynthesis protein Mog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7264
Polymers59,7033
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-47 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.132, 66.310, 74.332
Angle α, β, γ (deg.)92.15, 103.64, 119.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Molybdenum cofactor biosynthesis protein Mog


Mass: 19900.959 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: mog, SO_0065 / Plasmid: PMCSG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) DERIVATIVE / References: UniProt: Q8EKM7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 893 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M K THIOCYANATE 30 % PEGMME 2000, PH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97956 / Wavelength: 0.97956 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2005
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. all: 82328 / Num. obs: 79669 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 30.61
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 5.35 / Num. unique all: 7736 / % possible all: 94.7

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.89→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.796 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21633 3987 5 %RANDOM
Rwork0.17684 ---
all-79668 --
obs-79668 96.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.222 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0.17 Å2-0.15 Å2
2---0.85 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.89→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7863 0 3 893 8759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228103
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.32.00111026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.18951050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97925.016317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.865151422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5231549
X-RAY DIFFRACTIONr_chiral_restr0.0870.21291
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226049
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_it0.6041.55234
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09728536
X-RAY DIFFRACTIONr_scbond_it2.21232869
X-RAY DIFFRACTIONr_scangle_it3.3794.52490
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 254 -
Rwork0.193 4932 -
obs--84.27 %
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)
13.0288-0.40051.01121.3602-0.29031.3582-0.05890.1932-0.06470.06440.02680.1116-0.02270.09740.0320.0662-0.0025-0.00070.0861-0.00550.030511.600928.062863.8283
26.64040.57750.94792.0762-0.21731.7251-0.1568-0.75310.73260.33570.03890.0907-0.198-0.07350.11790.12590.0385-0.01660.0932-0.08150.081514.705537.983874.3048
33.0596-0.24621.02282.0714-0.00031.98430.04540.2219-0.0391-0.0498-0.07720.0933-0.0569-0.03230.03180.08090.0104-0.00120.1084-0.01080.005736.531321.490398.4767
43.9565-0.30770.7332.8029-0.05451.9676-0.0964-0.44220.56990.3009-0.0305-0.011-0.2005-0.18930.12690.08280.0176-0.01350.0641-0.06760.083238.551831.5368109.5704
52.27-0.3115-0.22011.6104-0.1880.9628-0.08470.18540.0021-0.20650.0408-0.15160.03150.02050.04390.1215-0.03070.00230.11240.00290.026440.293824.267861.9534
61.88960.2223-0.21733.24550.28981.473-0.0377-0.2072-0.16350.2271-0.0019-0.44760.08970.18610.03950.02180.0067-0.02370.0770.01080.078648.156418.092972.6836
73.2768-0.7185-0.79441.1959-0.21561.82450.03620.18140.3169-0.1477-0.0166-0.26670.08560.0448-0.01960.09530.00040.0230.08260.03930.082365.491618.199399.4275
82.1638-0.2558-0.58082.8205-0.09742.9950.0514-0.26830.05250.1543-0.0161-0.3130.22250.3302-0.03530.04030.0225-0.02840.0815-0.01020.045372.08211.5452110.7053
91.27220.1112-0.05452.58270.60641.4664-0.0090.0406-0.1958-0.1346-0.01150.1942-0.0042-0.00240.02050.0560.00310.01260.0277-0.00820.093322.99191.258463.0579
102.8248-1.52660.12084.98030.46651.2909-0.1165-0.2856-0.36530.65530.08140.64780.1947-0.07550.0350.1082-0.00470.09440.03940.04510.178914.7954-1.813374.6486
113.7665-1.6233-0.08563.67720.79562.44670.21180.2669-1.1128-0.2664-0.23170.71360.13150.00520.01990.08210.0181-0.07840.0253-0.08970.349348.2446-4.399498.2455
123.4704-3.4770.68964.46430.77832.3701-0.2096-0.3212-1.11440.53040.19541.2340.4947-0.27090.01420.2304-0.07770.15230.09030.13430.679538.9288-8.1644108.8498
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 18
2X-RAY DIFFRACTION1A40 - 135
3X-RAY DIFFRACTION2A19 - 39
4X-RAY DIFFRACTION2A136 - 174
5X-RAY DIFFRACTION3B3 - 18
6X-RAY DIFFRACTION3B40 - 135
7X-RAY DIFFRACTION4B19 - 39
8X-RAY DIFFRACTION4B136 - 174
9X-RAY DIFFRACTION5C2 - 18
10X-RAY DIFFRACTION5C40 - 135
11X-RAY DIFFRACTION6C19 - 39
12X-RAY DIFFRACTION6C136 - 174
13X-RAY DIFFRACTION7D3 - 18
14X-RAY DIFFRACTION7D40 - 135
15X-RAY DIFFRACTION8D19 - 39
16X-RAY DIFFRACTION8D136 - 174
17X-RAY DIFFRACTION9E3 - 18
18X-RAY DIFFRACTION9E40 - 135
19X-RAY DIFFRACTION10E19 - 39
20X-RAY DIFFRACTION10E136 - 173
21X-RAY DIFFRACTION11F4 - 18
22X-RAY DIFFRACTION11F40 - 135
23X-RAY DIFFRACTION12F19 - 39
24X-RAY DIFFRACTION12F136 - 173

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