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- PDB-3jqj: Crystal structure of the molybdenum cofactor biosynthesis protein... -

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Basic information

Entry
Database: PDB / ID: 3jqj
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 / Molybdenum cofactor biosynthesis
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
R-1,2-PROPANEDIOL / PHOSPHATE ION / Cyclic pyranopterin monophosphate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKanaujia, S.P. / Jeyakanthan, J. / Nakagawa, N. / Sekar, K. / Baba, S. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structures of apo and GTP-bound molybdenum cofactor biosynthesis protein MoaC from Thermus thermophilus HB8
Authors: Kanaujia, S.P. / Jeyakanthan, J. / Nakagawa, N. / Balasubramaniam, S. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Sekar, K.
History
DepositionSep 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 1, 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
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)206,36746
Polymers203,36112
Non-polymers3,00634
Water21,2761181
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)103,18323
Polymers101,6806
Non-polymers1,50317
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25850 Å2
ΔGint-155 kcal/mol
Surface area27460 Å2
MethodPISA
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)103,18323
Polymers101,6806
Non-polymers1,50317
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25620 Å2
ΔGint-149 kcal/mol
Surface area27560 Å2
MethodPISA
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

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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 / Gene: TTHA1789 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / 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: Chemical
ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1181 / 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: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 25%, 1,2-PROPANEDIOL, 5% PEG 3000, 0.1M PHOSPHATE-CITRATE PH 4.2, 10% GLYCEROL,, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 7, 2006 / Details: RH COATED BENT-CYLINDRICAL MIRROR
RadiationMonochromator: SI-111 DOUBLE CRYSTAL / 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 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.042
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.172 / Num. unique all: 12072 / Rsym value: 0.174 / % possible all: 99.7

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Processing

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

1ekr


Resolution: 1.9→49.66 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 604951.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.219 6078 5 %RANDOM
Rwork0.188 ---
obs0.188 120366 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.0318 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å20.56 Å2
2--4.13 Å20 Å2
3----1.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13218 0 182 1181 14581
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.243 987 5.2 %
Rwork0.208 17836 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramion.top
X-RAY DIFFRACTION3ion.paramwater_protin.top
X-RAY DIFFRACTION4ligand.paramligand.top

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