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- PDB-3kzq: The crystal structure of the protein with unknown function from V... -

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Basic information

Entry
Database: PDB / ID: 3kzq
TitleThe crystal structure of the protein with unknown function from Vibrio parahaemolyticus RIMD 2210633
ComponentsPutative uncharacterized protein VP2116
KeywordsStructural Genomics / Unknown function / Protein with unknown function / Vibrio parahaemolyticus / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyThioredoxin / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Chem-PG6 / DSBA-like thioredoxin domain-containing protein
Function and homology information
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhang, R. / Weger, A. / Shackelford, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the protein with unknown function from Vibrio parahaemolyticus RIMD 2210633
Authors: Zhang, R. / Weger, A. / Shackelford, G. / Joachimiak, A.
History
DepositionDec 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: 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_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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr1_auth_asym_id / _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_asym_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_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: Putative uncharacterized protein VP2116
B: Putative uncharacterized protein VP2116
C: Putative uncharacterized protein VP2116
D: Putative uncharacterized protein VP2116
E: Putative uncharacterized protein VP2116
F: Putative uncharacterized protein VP2116
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,15924
Polymers143,7276
Non-polymers2,43218
Water17,366964
1
A: Putative uncharacterized protein VP2116
E: Putative uncharacterized protein VP2116
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9997
Polymers47,9092
Non-polymers1,0905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-7 kcal/mol
Surface area20400 Å2
MethodPISA
2
B: Putative uncharacterized protein VP2116
hetero molecules

F: Putative uncharacterized protein VP2116
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5249
Polymers47,9092
Non-polymers6167
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_674-x+3/2,-y+2,z-1/21
Buried area2740 Å2
ΔGint-31 kcal/mol
Surface area20510 Å2
MethodPISA
3
C: Putative uncharacterized protein VP2116
hetero molecules

D: Putative uncharacterized protein VP2116
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6368
Polymers47,9092
Non-polymers7276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_644-x+1,y-1/2,-z-1/21
Buried area2110 Å2
ΔGint-14 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.304, 118.108, 206.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative uncharacterized protein VP2116


Mass: 23954.479 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: GI:28807109, VP2116 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q87MW5
#2: Chemical
ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26O6
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 964 / 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: 3.66 Å3/Da / Density % sol: 66.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG8000, 0.1M Tris, 0.2M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 6, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→102.54 Å / Num. all: 117520 / Num. obs: 115617 / % possible obs: 98.38 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 16.45
Reflection shellResolution: 2.1→2.155 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.18 / Num. unique all: 9082 / % possible all: 93.44

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→31.782 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.228 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.153 / ESU R Free: 0.146
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21836 6103 5 %RANDOM
Rwork0.17935 ---
obs0.18132 115617 98.38 %-
all-117520 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--0.61 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10026 0 151 964 11141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02210417
X-RAY DIFFRACTIONr_angle_refined_deg2.1491.97614095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96551230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.06225.432486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.712151806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7891530
X-RAY DIFFRACTIONr_chiral_restr0.1550.21512
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217812
X-RAY DIFFRACTIONr_mcbond_it1.1351.56186
X-RAY DIFFRACTIONr_mcangle_it2.163210044
X-RAY DIFFRACTIONr_scbond_it4.11134231
X-RAY DIFFRACTIONr_scangle_it6.1844.54051
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 441 -
Rwork0.227 8045 -
obs-8486 93.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2296-0.86070.41593.4391-0.65931.505-0.08750.1704-0.18670.17190.10.2576-0.08230.0078-0.01250.07750.05390.02410.09-0.0050.072533.49396.63342.393
20.874-0.0043-0.12910.8367-0.15791.1393-0.006-0.0061-0.06950.03660.0223-0.04950.0521-0.034-0.01630.05440.0199-0.0020.05980.00890.01674.493131.55211.374
30.73490.17750.11531.3260.91091.46750.0248-0.0567-0.0539-0.03460.0183-0.04730.0410.0647-0.04310.08670.004-0.03140.0527-0.02590.032134.078118.747-29.314
41.8732-0.8856-0.89792.34971.13661.80610.01750.15570.0870.0421-0.0454-0.07240.0656-0.14830.02780.04940.0192-0.00050.0537-0.00810.011639.164124.85-65.934
51.121-0.0390.10870.6793-0.07070.80320.0382-0.0397-0.05690.0265-0.01930.04030.04060.0148-0.0190.078-0.004-0.01520.09290.00470.006646.61131.0692.769
61.2362-0.14880.09391.4865-0.40350.924-0.03110.01160.05430.04690.0073-0.0082-0.06080.10090.02390.0775-0.01710.00390.03420.03010.043237.631122.8467.74
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 206
2X-RAY DIFFRACTION2B1 - 206
3X-RAY DIFFRACTION3C1 - 206
4X-RAY DIFFRACTION4D1 - 206
5X-RAY DIFFRACTION5E1 - 206
6X-RAY DIFFRACTION6F1 - 206

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