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- PDB-2qip: Crystal structure of a protein of unknown function VPA0982 from V... -

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Basic information

Entry
Database: PDB / ID: 2qip
TitleCrystal structure of a protein of unknown function VPA0982 from Vibrio parahaemolyticus RIMD 2210633
ComponentsProtein of unknown function VPA0982
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC85975 / VPA0982 / Vibrio parahaemolyticus RIMD 2210633 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology: / NYN domain, MARF1-type / NYN domain / 5'-nuclease / RNA nuclease activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NYN domain-containing protein
Function and homology information
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 Å
AuthorsTan, K. / Duggan, E. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a protein of unknown function, VPA0982 from Vibrio parahaemolyticus RIMD 2210633.
Authors: Tan, K. / Duggan, E. / Moy, S. / Joachimiak, A.
History
DepositionJul 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN AT THE TIME OF DEPOSITION. FROM MOLECULAR PACKING IT SEEMS TO FORM A DIMER WITH ITS SYMMETRY-RELATED MOLECULE. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein of unknown function VPA0982
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3607
Polymers18,9881
Non-polymers3726
Water3,207178
1
A: Protein of unknown function VPA0982
hetero molecules

A: Protein of unknown function VPA0982
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,72114
Polymers37,9762
Non-polymers74512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)62.207, 75.034, 80.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-354-

HOH

DetailsExperimentally unknown. From molecular packing, it seems to form a dimer with its symmetry-related molecule (1-x,1-y,z).

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Components

#1: Protein Protein of unknown function VPA0982


Mass: 18988.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VPA0982 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9AF14
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M Ammonium sulfate, 0.1M Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2007 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.48→24.62 Å / Num. all: 31578 / Num. obs: 31578 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 45.96
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.73 / Num. unique all: 1482 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.48→24.62 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.833 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.075 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18312 1594 5 %RANDOM
Rwork0.16237 ---
all0.16346 29978 --
obs0.16346 29978 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.619 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.48→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 24 178 1515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221371
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.361.951849
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06324.38473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53915233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7741510
X-RAY DIFFRACTIONr_chiral_restr0.1430.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021049
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2594
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2953
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2831.5835
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93821318
X-RAY DIFFRACTIONr_scbond_it4.5783608
X-RAY DIFFRACTIONr_scangle_it4.4744.5529
X-RAY DIFFRACTIONr_rigid_bond_restr5.03931443
X-RAY DIFFRACTIONr_sphericity_free4.5753178
X-RAY DIFFRACTIONr_sphericity_bonded3.78231349
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 101 -
Rwork0.196 2085 -
obs-2186 94.92 %

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