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- PDB-1wu2: Crystal Structure of molybdopterin biosynthesis moeA protein from... -

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Basic information

Entry
Database: PDB / ID: 1wu2
TitleCrystal Structure of molybdopterin biosynthesis moeA protein from Pyrococcus horikoshii OT3
Componentsmolybdopterin biosynthesis moeA protein
KeywordsSTRUCTURAL GENOMICS / BIOSYNTHETIC PROTEIN / moeA protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


molybdopterin cofactor biosynthetic process / Mo-molybdopterin cofactor biosynthetic process
Similarity search - Function
Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdopterin biosynthesis moea protein, domain 2 / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like ...Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdopterin biosynthesis moea protein, domain 2 / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdopterin biosynthesis moea protein, domain 2 / 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 / Beta Complex / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / 396aa long hypothetical molybdopterin biosynthesis moeA protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLokanath, N.K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of molybdopterin biosynthesis moeA protein from Pyrococcus horikoshii OT3
Authors: Lokanath, N.K. / Kunishima, N.
History
DepositionNov 30, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: molybdopterin biosynthesis moeA protein
B: molybdopterin biosynthesis moeA protein


Theoretical massNumber of molelcules
Total (without water)88,9582
Polymers88,9582
Non-polymers00
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-29 kcal/mol
Surface area34670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.149, 65.912, 76.684
Angle α, β, γ (deg.)90.00, 102.17, 90.00
Int Tables number5
Space group name H-MC121
DetailsBiological assembly is dimer

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Components

#1: Protein molybdopterin biosynthesis moeA protein / moeA protein


Mass: 44479.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (DE3)-RIL / References: GenBank: 14591417, UniProt: O59354*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 295 K / Method: microbacth / pH: 7.6
Details: PEG 4k, HEPES, pH 7.6, microbacth, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97904, 0.97939, 1.0
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 8, 2004 / Details: RH coated bent-cylindrical mirror
RadiationMonochromator: SI111 double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979041
20.979391
311
ReflectionResolution: 2.3→40 Å / Num. all: 36236 / Num. obs: 35136 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.887 / SU B: 9.72 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.45 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28226 1857 5 %RANDOM
Rwork0.23321 ---
obs0.23574 35136 98.1 %-
all-36236 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.141 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å20.23 Å2
2---0.03 Å20 Å2
3----2.65 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5978 0 0 423 6401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226085
X-RAY DIFFRACTIONr_bond_other_d0.0010.025793
X-RAY DIFFRACTIONr_angle_refined_deg0.9431.9888219
X-RAY DIFFRACTIONr_angle_other_deg0.712313526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615758
X-RAY DIFFRACTIONr_chiral_restr0.0580.2943
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021137
X-RAY DIFFRACTIONr_nbd_refined0.1610.21096
X-RAY DIFFRACTIONr_nbd_other0.1950.26804
X-RAY DIFFRACTIONr_nbtor_other0.0790.23794
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.23
X-RAY DIFFRACTIONr_mcbond_it0.4051.53785
X-RAY DIFFRACTIONr_mcangle_it0.74926144
X-RAY DIFFRACTIONr_scbond_it0.67332300
X-RAY DIFFRACTIONr_scangle_it1.2154.52075
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 141
Rwork0.283 2445

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