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- PDB-2ide: Crystal Structure of the molybdenum cofactor biosynthesis protein... -

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Basic information

Entry
Database: PDB / ID: 2ide
TitleCrystal Structure of the molybdenum cofactor biosynthesis protein C (TTHA1789) from Thermus Theromophilus HB8
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: 1.9 Å
AuthorsJeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Baba, S. / 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
Authors: Jeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Baba, S. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S.
History
DepositionSep 15, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 25, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein C
B: Molybdenum cofactor biosynthesis protein C
C: Molybdenum cofactor biosynthesis protein C
D: Molybdenum cofactor biosynthesis protein C
E: Molybdenum cofactor biosynthesis protein C
F: Molybdenum cofactor biosynthesis protein C
G: Molybdenum cofactor biosynthesis protein C
H: Molybdenum cofactor biosynthesis protein C
I: Molybdenum cofactor biosynthesis protein C
J: Molybdenum cofactor biosynthesis protein C
K: Molybdenum cofactor biosynthesis protein C
L: Molybdenum cofactor biosynthesis protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,50124
Polymers203,36112
Non-polymers1,14012
Water28,5361584
1
A: Molybdenum cofactor biosynthesis protein C
B: Molybdenum cofactor biosynthesis protein C
C: Molybdenum cofactor biosynthesis protein C
D: Molybdenum cofactor biosynthesis protein C
E: Molybdenum cofactor biosynthesis protein C
F: Molybdenum cofactor biosynthesis protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,25012
Polymers101,6806
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22730 Å2
ΔGint-187 kcal/mol
Surface area28170 Å2
MethodPISA, PQS
2
G: Molybdenum cofactor biosynthesis protein C
H: Molybdenum cofactor biosynthesis protein C
I: Molybdenum cofactor biosynthesis protein C
J: Molybdenum cofactor biosynthesis protein C
K: Molybdenum cofactor biosynthesis protein C
L: Molybdenum cofactor biosynthesis protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,25012
Polymers101,6806
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22730 Å2
ΔGint-177 kcal/mol
Surface area28530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.809, 109.836, 115.192
Angle α, β, γ (deg.)90.00, 104.86, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe crystallographic symmetric unit which consists of 12 monomers (A,B,C,D,E,F,G,H,I,J, K,L). Biological unit is hexamer

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Components

#1: Protein
Molybdenum cofactor biosynthesis protein C


Mass: 16946.742 Da / Num. of mol.: 12
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


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1584 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 25%, 1,2-propanediol, 5% PEG3000, 0.1M phosphate-citrate pH 4.2, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 7, 2006 / Details: RH Coated Bent-Cyrindrical Mirror
RadiationMonochromator: SI-111 Double crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 121501 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.042 / Rsym value: 0.045
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.174 / Num. unique all: 12072 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EKR

1ekr


Resolution: 1.9→49.66 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 6049516.53 / 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
Rfree0.226 6078 5 %RANDOM
Rwork0.195 ---
obs0.195 120366 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.4329 Å2 / ksol: 0.360197 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20.41 Å2
2--4.03 Å20 Å2
3----2.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13206 0 60 1584 14850
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.257 733 5.3 %
Rwork0.228 13058 -
obs--90.4 %
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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