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- PDB-5ir0: Crystal structure of protein of unknown function ORF19 from Vibri... -

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Basic information

Entry
Database: PDB / ID: 5ir0
TitleCrystal structure of protein of unknown function ORF19 from Vibrio cholerae O1 PICI-like element, C57S I109M mutant
ComponentsUncharacterized protein ORF19
KeywordsUNKNOWN FUNCTION / Vibrio cholerae / alpha/beta protein / structure genomics / Center for Structural Genomics of Infectious Diseases / CSGID / National Institutes of Allergy and Infectious Diseases / NIAID
Function / homology: / Phage tail assembly chaperone protein, TAC / CITRIC ACID / Uncharacterized protein
Function and homology information
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.297 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Skarina, T. / Di Leo, R. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of protein of unknown function ORF19 from Vibrio cholerae O1 PICI-like element, C57S I109M mutant
Authors: Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein ORF19
B: Uncharacterized protein ORF19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8713
Polymers36,6792
Non-polymers1921
Water724
1
A: Uncharacterized protein ORF19


Theoretical massNumber of molelcules
Total (without water)18,3401
Polymers18,3401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein ORF19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5322
Polymers18,3401
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.852, 126.852, 51.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Uncharacterized protein ORF19


Mass: 18339.510 Da / Num. of mol.: 2 / Mutation: C57S, I109M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M1Q7T5
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M citrate, 20% PEG3350, cryoprotectant 5% PEG200, paratone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.297→25 Å / % possible obs: 97.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 34.65
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 3.57 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 3.297→24.859 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.57 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2932 950 9.99 %Random
Rwork0.2375 ---
obs0.243 9505 78.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.297→24.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 13 4 1683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061711
X-RAY DIFFRACTIONf_angle_d1.0472316
X-RAY DIFFRACTIONf_dihedral_angle_d13.823619
X-RAY DIFFRACTIONf_chiral_restr0.045271
X-RAY DIFFRACTIONf_plane_restr0.006287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2967-3.470.355620.275561X-RAY DIFFRACTION36
3.47-3.68680.3325930.263876X-RAY DIFFRACTION55
3.6868-3.97040.29931310.22261187X-RAY DIFFRACTION76
3.9704-4.3680.29051590.21591416X-RAY DIFFRACTION91
4.368-4.99560.24741640.21951509X-RAY DIFFRACTION97
4.9956-6.27720.28911690.24831537X-RAY DIFFRACTION98
6.2772-24.85980.31121720.25211469X-RAY DIFFRACTION95
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)
12.0135-2.15270.33343.6553-1.13880.6270.21320.0714-0.3399-0.5252-0.12770.29450.1130.0365-0.17670.2877-0.1089-0.24380.14690.1780.543760.697733.047619.739
25.427-2.9515-3.63417.39987.91598.58550.0680.3523-0.5510.40230.0926-0.00350.42310.3898-0.17391.00180.1947-0.04580.71730.20031.48257.278915.016215.1235
30.0150.0436-0.00750.1326-0.02760.04130.031-0.0025-0.025-0.02370.01560.07890.089-0.03880.11040.2613-0.0489-0.31230.02690.23270.46351.321933.104921.2395
40.99160.07871.09860.3249-0.03721.2653-0.00330.5513-0.3598-0.46370.023-0.5434-0.25770.1967-0.02510.44480.1080.26750.77180.20690.601370.076934.360912.5071
52.6888-2.63251.35938.7257-0.83287.22570.155-0.1068-0.1993-0.1150.18840.361-0.3668-0.5396-0.25850.43180.0676-0.11950.22730.10040.730231.293224.773416.3765
60.9777-0.5650.18280.7964-0.56490.70040.07930.1440.0018-0.1149-0.08120.069-0.1207-0.1031-0.18270.44780.1114-0.29670.19160.16460.403840.437720.780512.0574
71.2523-0.233-0.3432.7791-0.65881.4117-0.2230.0154-0.06050.098-0.09590.3468-0.1161-0.039-0.28020.26110.1904-0.18470.0734-0.08180.383534.739215.911912.6631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:41)
2X-RAY DIFFRACTION2(chain A and resid 67:71)
3X-RAY DIFFRACTION3(chain A and resid 72:120)
4X-RAY DIFFRACTION4(chain A and resid 121:126)
5X-RAY DIFFRACTION5(chain B and resid 0:11)
6X-RAY DIFFRACTION6(chain B and resid 12:40)
7X-RAY DIFFRACTION7(chain B and resid 67:128)

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