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- PDB-2iih: Crystal structure of the molybdenum cofactor biosynthesis protein... -

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Basic information

Entry
Database: PDB / ID: 2iih
TitleCrystal structure of the molybdenum cofactor biosynthesis protein C (TTHA1789) from thermus theromophilus HB8 (H32 form)
ComponentsMolybdenum cofactor biosynthesis protein C
KeywordsBIOSYNTHETIC PROTEIN / MOAC / MOLYBDENUM COFACTOR (MOCO) / MOCO BIOSYNTHESIS / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cyclic pyranopterin monophosphate synthase / cyclic pyranopterin monophosphate synthase activity / Mo-molybdopterin cofactor biosynthetic process / GTP binding
Similarity search - Function
: / Molybdopterin cofactor biosynthesis C (MoaC) domain / Molybdopterin cofactor biosynthesis C (MoaC) domain / Molybdenum cofactor biosynthesis C / Molybdopterin cofactor biosynthesis C (MoaC) domain superfamily / MoaC family / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Cyclic pyranopterin monophosphate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Baba, S. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Ebihara, A. / Kuramitsu, S. ...Jeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Baba, S. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the molybdenum cofactor biosynthesis protein C (TTHA1789) from thermus theromophilus HB8 (H32 form)
Authors: Jeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Baba, S. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S.
History
DepositionSep 28, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Molybdenum cofactor biosynthesis protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0422
Polymers16,9471
Non-polymers951
Water3,081171
1
A: Molybdenum cofactor biosynthesis protein C
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)102,25012
Polymers101,6806
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area22590 Å2
ΔGint-205 kcal/mol
Surface area27720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.573, 106.573, 59.251
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-444-

HOH

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Components

#1: Protein Molybdenum cofactor biosynthesis protein C


Mass: 16946.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHE1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.91 Å3/Da / Density % sol: 35.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M Na Acetate, 1.0M Ammonium H2 phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97243 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2006 / Details: mirrors
RadiationMonochromator: SI111 Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 13115 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.08
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.175 / Num. unique all: 1288 / Rsym value: 0.177 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IDE

2ide


Resolution: 1.75→23.5 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1753647.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 667 5.1 %RANDOM
Rwork0.196 ---
obs0.196 12995 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.7304 Å2 / ksol: 0.373194 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0.55 Å20 Å2
2--0.33 Å20 Å2
3----0.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.75→23.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 5 171 1268
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 1.75→1.83 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.287 89 5.6 %
Rwork0.25 1500 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION5water_rep.paramwater_protin.top

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