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- PDB-2yx6: Crystal structure of PH0822 -

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Basic information

Entry
Database: PDB / ID: 2yx6
TitleCrystal structure of PH0822
ComponentsHypothetical protein PH0822
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


MTH1175 domain / : / Dinitrogenase iron-molybdenum cofactor biosynthesis domain / Dinitrogenase iron-molybdenum cofactor biosynthesis / Dinitrogenase iron-molybdenum cofactor biosynthesis superfamily / Dinitrogenase iron-molybdenum cofactor / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Dinitrogenase iron-molybdenum cofactor biosynthesis domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHosaka, T. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of PH0822
Authors: Hosaka, T. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionApr 24, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein PH0822
B: Hypothetical protein PH0822
C: Hypothetical protein PH0822
D: Hypothetical protein PH0822
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1865
Polymers54,7584
Non-polymers4271
Water1,928107
1
A: Hypothetical protein PH0822

A: Hypothetical protein PH0822


Theoretical massNumber of molelcules
Total (without water)27,3792
Polymers27,3792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
B: Hypothetical protein PH0822
C: Hypothetical protein PH0822
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8063
Polymers27,3792
Non-polymers4271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Hypothetical protein PH0822

D: Hypothetical protein PH0822


Theoretical massNumber of molelcules
Total (without water)27,3792
Polymers27,3792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)94.932, 99.877, 48.812
Angle α, β, γ (deg.)90.00, 112.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Hypothetical protein PH0822


Mass: 13689.595 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: O58552
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 37.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG8000, 0.01M imidazole, 0.01M adenosine-5-triphosphate disodium salt, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 29, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 21963 / % possible obs: 77.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.75782 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.06 / Net I/σ(I): 15.8657
Reflection shellResolution: 2→2.09 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 4.51497 / Num. unique all: 1444 / Rsym value: 0.144 / % possible all: 40.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O13

1o13


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.514 / SU ML: 0.157 / Data cutoff high absF: 2182298.8 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26242 1084 4.9 %RANDOM
Rwork0.21419 ---
obs0.21666 20849 77.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.102 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.12 Å2
2--0.53 Å20 Å2
3----0.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.12 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3529 0 27 107 3663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223628
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.9624883
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5835435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24523.195169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.31315632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1851527
X-RAY DIFFRACTIONr_chiral_restr0.1370.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022716
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.21601
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3310.22462
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3851.52226
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.17223514
X-RAY DIFFRACTIONr_scbond_it3.26331598
X-RAY DIFFRACTIONr_scangle_it4.9294.51369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 39 -
Rwork0.212 676 -
obs--34.24 %

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