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- PDB-1vjk: Putative molybdopterin converting factor, subunit 1 from Pyrococc... -

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Basic information

Entry
Database: PDB / ID: 1vjk
TitlePutative molybdopterin converting factor, subunit 1 from Pyrococcus furiosus, Pfu-562899-001
Componentsmolybdopterin converting factor, subunit 1
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / molybdopterin converting factor / subunit 1 / Pfu-562899-001 / Pyrococcus furiosus / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process / nucleotide binding
Similarity search - Function
MoaD, archaeal-type / Molybdopterin synthase sulfur carrier subunit / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Molybdopterin synthase sulfur carrier subunit
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.51 Å
AuthorsChen, L. / Liu, Z.J. / Tempel, W. / Shah, A. / Lee, D. / Rose, J.P. / Eneh, J.C. / Hopkins, R.C. / Jenney Jr., F.E. / Lee, H.S. ...Chen, L. / Liu, Z.J. / Tempel, W. / Shah, A. / Lee, D. / Rose, J.P. / Eneh, J.C. / Hopkins, R.C. / Jenney Jr., F.E. / Lee, H.S. / Li, T. / Poole II, F.L. / Shah, C. / Sugar, F.J. / Adams, M.W.W. / Richardson, D.C. / Richardson, J.S. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Putative molybdopterin converting factor, subunit 1 from Pyrococcus furiosus, Pfu-562899-001 '
Authors: Chen, L. / Liu, Z.J. / Tempel, W. / Shah, A. / Lee, D. / Rose, J.P. / ENEH, J.C. / HOPKINS, R.C. / JENNEY JR., F.E. / LEE, H.S. / Li, T. / POOLE II, F.L. / SHAH, C. / SUGAR, F.J. / ADAMS, M. ...Authors: Chen, L. / Liu, Z.J. / Tempel, W. / Shah, A. / Lee, D. / Rose, J.P. / ENEH, J.C. / HOPKINS, R.C. / JENNEY JR., F.E. / LEE, H.S. / Li, T. / POOLE II, F.L. / SHAH, C. / SUGAR, F.J. / ADAMS, M.W.W. / Richardson, D.C. / Richardson, J.S. / Wang, B.C. / Southeast Collaboratory for Structural Genomics
History
DepositionMar 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: molybdopterin converting factor, subunit 1


Theoretical massNumber of molelcules
Total (without water)11,2011
Polymers11,2011
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.467, 81.467, 63.698
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein molybdopterin converting factor, subunit 1


Mass: 11201.399 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea)
Description: THE PROTEIN WAS CLONED, EXPRESSED AND PURIFIED BY THE SECSG PYROCOCCUS PROTEIN PRODUCTION GROUP (M.W.W.ADAMS, P.S.BRERETON, M.IZUMI, F.E.JENNEY JR., H.- S.LEE, F.L.POOLE II, C.SHAH, F. ...Description: THE PROTEIN WAS CLONED, EXPRESSED AND PURIFIED BY THE SECSG PYROCOCCUS PROTEIN PRODUCTION GROUP (M.W.W.ADAMS, P.S.BRERETON, M.IZUMI, F.E.JENNEY JR., H.- S.LEE, F.L.POOLE II, C.SHAH, F.SUGAR) UNDER THE DIRECTION OF M.W.W.ADAMS.
Production host: Escherichia coli (E. coli) / References: UniProt: Q8U3C7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 291 K / Method: modified microbatch / pH: 6.5
Details: 100mM sodium cacodylate, 30% PEG 8000, 200mM ammonium sulfate, modified microbatch, temperature 291K, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 19993 / % possible obs: 99.3 % / Rmerge(I) obs: 0.065
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
1.51-1.560.161100
1.56-1.630.1321100
1.63-1.70.1081100
1.7-1.790.0911100
1.79-1.90.0771100
1.9-2.050.0671100
2.05-2.260.0631100
2.26-2.580.0611100
2.58-3.250.065199.9
3.25-500.058193.3

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 20 Å / FOM : 0.42 / Reflection: 4584
Phasing MAD shell
Resolution (Å)FOM Reflection
8.52-200.35272
5.54-8.520.41404
4.38-5.540.42498
3.74-4.380.43559
3.31-3.740.46636
3-3.310.44687
2.77-30.43745
2.58-2.770.41783
Phasing dmFOM : 0.59 / FOM acentric: 0.62 / FOM centric: 0.49 / Reflection: 5819 / Reflection acentric: 4568 / Reflection centric: 1251
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-19.540.830.830.64291149142
4.1-6.60.80.860.64821571250
3.3-4.10.80.840.64982762220
2.9-3.30.70.750.5973779194
2.5-2.90.540.580.3317051415290
2.3-2.50.180.180.161047892155

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Processing

Software
NameVersionClassificationNB
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefmac_5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT1data extraction
ARP/wARPmodel building
XFITdata reduction
MolProbitymodel building
RefinementResolution: 1.51→70.711 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.934 / SU B: 0.954 / SU ML: 0.037 / SU R Cruickshank DPI: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.07
Details: Difference density close to the sidechains of residues TYR 54 and TYR 68 suggests the presence of the crystallization reagent polyethylene glycol between symmetry-related copies of the peptide chain.
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1021 5.116 %RANDOM
Rwork0.21 ---
all0.211 ---
obs-18936 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 13.587 Å2
Baniso -1Baniso -2Baniso -3
1-0.225 Å20.112 Å20 Å2
2--0.225 Å20 Å2
3----0.337 Å2
Refinement stepCycle: LAST / Resolution: 1.51→70.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms702 0 0 67 769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021715
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.954964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.951586
X-RAY DIFFRACTIONr_chiral_restr0.090.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02561
X-RAY DIFFRACTIONr_nbd_refined0.1930.2255
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2489
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0750.247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.28
X-RAY DIFFRACTIONr_mcbond_it1.8632431
X-RAY DIFFRACTIONr_mcangle_it2.8343694
X-RAY DIFFRACTIONr_scbond_it2.8172284
X-RAY DIFFRACTIONr_scangle_it4.4313270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.51-1.54910.206820.17613681450
1.549-1.59150.178830.17413381421
1.591-1.63760.205670.17613051372
1.638-1.6880.285640.19712691333
1.688-1.74330.25570.19712411298
1.743-1.80440.218640.19912141278
1.804-1.87250.19630.19211501213
1.873-1.94890.204600.19811201180
1.949-2.03550.221620.20710811143
2.036-2.13480.222530.2110291082
2.135-2.25010.215540.2099771032
2.25-2.38650.226530.209931987
2.386-2.5510.252540.229876930
2.551-2.75510.253400.221829869
2.755-3.01770.227430.227770813
3.018-3.37310.218440.23687734
3.373-3.89340.213270.201593656
3.893-4.76480.207190.185531573
4.765-6.72320.226180.23422458
6.723-70.71070.286140.31205288
Refinement TLS params.Method: refined / Origin x: 31.841 Å / Origin y: 44.319 Å / Origin z: 0.93 Å
111213212223313233
T0.0248 Å20.0225 Å2-0.0044 Å2-0.0887 Å20.0307 Å2--0.0212 Å2
L1.8303 °2-0.4511 °2-0.5906 °2-0.9073 °2-0.2207 °2--1.1329 °2
S-0.0827 Å °-0.0929 Å °-0.09 Å °0.0844 Å °0.0333 Å °0.0378 Å °-0.0414 Å °0.1577 Å °0.0495 Å °
Refinement TLS groupSelection: ALL

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