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- PDB-3i8n: A domain of a conserved functionally known protein from Vibrio pa... -

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Basic information

Entry
Database: PDB / ID: 3i8n
TitleA domain of a conserved functionally known protein from Vibrio parahaemolyticus RIMD 2210633.
Componentsuncharacterized protein VP2912
Keywordsstructural genomics / unknown function / APC64273.1 / Vibrio parahaemolyticus RIMD 2210633 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG.
Function / homology
Function and homology information


Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. ...Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Hemolysin
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.145 Å
AuthorsTan, K. / Tesar, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: A domain of a conserved functionally known protein from Vibrio parahaemolyticus RIMD 2210633.
Authors: Tan, K. / Tesar, C. / Bearden, J. / Joachimiak, A.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 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_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_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: uncharacterized protein VP2912
B: uncharacterized protein VP2912
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1034
Polymers30,0112
Non-polymers922
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: uncharacterized protein VP2912
hetero molecules

A: uncharacterized protein VP2912
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1034
Polymers30,0112
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area2420 Å2
ΔGint-9 kcal/mol
Surface area12630 Å2
MethodPISA
3
B: uncharacterized protein VP2912
hetero molecules

B: uncharacterized protein VP2912
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1034
Polymers30,0112
Non-polymers922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area1350 Å2
ΔGint-9 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.301, 69.301, 255.136
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsExperimentally unknown. The chains A and B may form a dimer.

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Components

#1: Protein uncharacterized protein VP2912


Mass: 15005.357 Da / Num. of mol.: 2 / Fragment: residues189-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: Vibrio parahaemolyticus, VP2912 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q87KR4
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris Propane 2.0M Sodium Format, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.145→50 Å / Num. all: 20653 / Num. obs: 20653 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 45.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 4.16 / Num. unique all: 1009 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.145→49.036 Å / SU ML: 0.34 / σ(F): 1.89 / σ(I): 0 / Stereochemistry target values: ML
Details: The number of reflections listed here treats f+ and f- separately.
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 1893 5.13 %random
Rwork0.219 ---
all0.2212 20653 --
obs0.2212 20653 98.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.327 Å2 / ksol: 0.354 e/Å3
Refinement stepCycle: LAST / Resolution: 2.145→49.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 0 113 2120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092051
X-RAY DIFFRACTIONf_angle_d1.1732784
X-RAY DIFFRACTIONf_dihedral_angle_d19.399772
X-RAY DIFFRACTIONf_chiral_restr0.073332
X-RAY DIFFRACTIONf_plane_restr0.005358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1449-2.19850.31631510.29992292229291
2.1985-2.25790.33041430.28892540254099
2.2579-2.32440.3021510.267825362536100
2.3244-2.39940.28721360.249225352535100
2.3994-2.48520.29141370.227125352535100
2.4852-2.58460.27821320.228725432543100
2.5846-2.70230.32911470.23825172517100
2.7023-2.84470.28721460.239325442544100
2.8447-3.02290.2851460.248125542554100
3.0229-3.25630.26731140.221325492549100
3.2563-3.58390.29181150.211825652565100
3.5839-4.10230.2571530.19542511251199
4.1023-5.16750.21541110.19162365236593
5.1675-49.04850.22231110.212447244795
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.598-0.78180.050.89610.65580.9877-0.0134-0.0329-0.09470.1580.02560.11710.29050.06280.01390.54330.09810.0350.49420.01790.481129.732624.979192.6214
21.09320.0587-1.15030.9933-0.56041.4857-0.1080.14720.01970.11760.0836-0.06760.33320.20290.00950.58190.1691-0.05950.53910.01360.3528
Refinement TLS groupSelection details: chain B

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