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- PDB-1vk1: Conserved hypothetical protein from Pyrococcus furiosus Pfu-392566-001 -

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Basic information

Entry
Database: PDB / ID: 1vk1
TitleConserved hypothetical protein from Pyrococcus furiosus Pfu-392566-001
ComponentsConserved hypothetical protein
Keywordsstructural genomics / unknown function / reductive methylation / dimethyl lysine / Pyrococcus furiosus / conserved hypothetical protein / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, domain 2 / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, domain 2 / Domain of unknown function DUF5603 / Domain of unknown function (DUF5603) / L-serine kinase SerK/SbnI, C-terminal / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain ...Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, domain 2 / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, domain 2 / Domain of unknown function DUF5603 / Domain of unknown function (DUF5603) / L-serine kinase SerK/SbnI, C-terminal / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SINGLE WAVELENGTH ANOMALOUS SCATTERING / MIR / Resolution: 1.2 Å
AuthorsShah, A. / Liu, Z.J. / Tempel, W. / Chen, L. / Lee, D. / Yang, H. / Chang, J. / Zhao, M. / Ng, J. / Rose, J. ...Shah, A. / Liu, Z.J. / Tempel, W. / Chen, L. / Lee, D. / Yang, H. / Chang, J. / Zhao, M. / Ng, J. / Rose, J. / Brereton, P.S. / Izumi, M. / Jenney Jr., F.E. / 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)
Citation
Journal: Bmc Struct.Biol. / Year: 2007
Title: (NZ)CH...O contacts assist crystallization of a ParB-like nuclease.
Authors: Shaw, N. / Cheng, C. / Tempel, W. / Chang, J. / Ng, J. / Wang, X.Y. / Perrett, S. / Rose, J. / Rao, Z. / Wang, B.C. / Liu, Z.J.
#1: Journal: Proteins / Year: 2008
Title: Crystal structure solution of a ParB-like nuclease at atomic resolution.
Authors: Shaw, N. / Tempel, W. / Chang, J. / Yang, H. / Cheng, C. / Ng, J. / Rose, J. / Rao, Z. / Wang, B.C. / Liu, Z.J.
History
DepositionApr 13, 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: Version format compliance
Revision 1.3Jan 9, 2013Group: Database references
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: Conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2174
Polymers27,9931
Non-polymers2243
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.148, 40.099, 65.671
Angle α, β, γ (deg.)90.00, 122.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Conserved hypothetical protein


Mass: 27992.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U3S5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 2.0M NaCl, 0.1M TRIS, pH 8.5, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.07
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / % possible obs: 80.5 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rsym value: 0.04 / Net I/σ(I): 34.3
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.14 / % possible all: 21.5

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Phasing

PhasingMethod: MIR
Phasing dmFOM : 0.62 / FOM acentric: 0.62 / FOM centric: 0.65 / Reflection: 10970 / Reflection acentric: 10184 / Reflection centric: 786
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-19.9550.820.820.81503403100
4.1-6.60.840.840.8215481383165
3.3-4.10.80.810.7219111763148
2.9-3.30.720.720.7218511745106
2.5-2.90.590.590.5432273057170
2.3-2.50.20.20.231930183397
Phasing MIRResolution: 2.5→20 Å / FOM: 0.54 / Reflection: 8671
Phasing MIR shell
Resolution (Å)FOMReflection
8.52-200.62473
5.54-8.520.63753
4.38-5.540.59934
3.74-4.380.541103
3.31-3.740.531215
3-3.310.531307
2.77-30.521425
2.58-2.770.51461

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefmac_5.2.0001refinement
ARP/wARPrefmac_5.2.0001model building
PDB_EXTRACT1data extraction
MolProbitymodel building
SCA2STRUCTUREPIPELINEphasing
RefinementMethod to determine structure: SINGLE WAVELENGTH ANOMALOUS SCATTERING
Resolution: 1.2→55.9 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.965 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.175 3374 5.1 %RANDOM
Rwork0.165 ---
obs0.166 63181 83.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.26 Å2
2--1.12 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.2→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 12 137 1992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221914
X-RAY DIFFRACTIONr_bond_other_d0.0020.021855
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9872586
X-RAY DIFFRACTIONr_angle_other_deg0.7434288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5682580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97115352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.897157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_nbd_refined0.2230.2310
X-RAY DIFFRACTIONr_nbd_other0.1660.21779
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.21173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1620.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0840.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.99121159
X-RAY DIFFRACTIONr_mcbond_other1.792471
X-RAY DIFFRACTIONr_mcangle_it2.79231877
X-RAY DIFFRACTIONr_scbond_it2.5142755
X-RAY DIFFRACTIONr_scangle_it3.7013709
X-RAY DIFFRACTIONr_rigid_bond_restr1.30133769
X-RAY DIFFRACTIONr_sphericity_free6.3743138
X-RAY DIFFRACTIONr_sphericity_bonded3.23933732
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.194 75
Rwork0.179 1369

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