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- PDB-5kvk: Crystal structure of the Competence-Damaged Protein (CinA) Superf... -

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Basic information

Entry
Database: PDB / ID: 5kvk
TitleCrystal structure of the Competence-Damaged Protein (CinA) Superfamily Protein KP700603 from Klebsiella pneumoniae 700603
ComponentsProtein KP700603
KeywordsUNKNOWN FUNCTION / CINA / COMPETENCE-DAMAGED PROTEIN / OUTER MEMBRANE BIOGENESIS / STRUCTURAL GENOMICS / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASE
Function / homologyCinA-like / CinA, C-terminal / CinA-like, C-terminal / Competence-damaged protein / Maf protein / Alpha-Beta Complex / Alpha Beta / Protein KP700603
Function and homology information
Biological speciesKlebsiella pneumoniae 700603 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Evdokimova, E. / Di Leo, R. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: To be published
Authors: Stogios, P.J.
History
DepositionJul 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein KP700603


Theoretical massNumber of molelcules
Total (without water)18,0701
Polymers18,0701
Non-polymers00
Water2,684149
1
A: Protein KP700603

A: Protein KP700603


Theoretical massNumber of molelcules
Total (without water)36,1402
Polymers36,1402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area1700 Å2
ΔGint-12 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.460, 38.460, 178.238
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 Protein KP700603


Mass: 18070.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae 700603 (bacteria)
Gene: KP700603 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1C7D1B5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence matches to GB WP_004206011.1 but this sequence is not yet available in UniProt.

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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: 1.82 Å3/Da / Density % sol: 32.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate pH 4.5, 30% PEG 300, 0.3 M NDSB 195

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.66→29.115 Å / Num. obs: 16307 / % possible obs: 96.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 52.37
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 3.08 / CC1/2: 0.68 / % possible all: 80.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KOL

5kol


Resolution: 1.66→29.115 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 813 5.01 %Random selection
Rwork0.1612 ---
obs0.1634 16241 96.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.66→29.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 0 149 1335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141247
X-RAY DIFFRACTIONf_angle_d1.4731705
X-RAY DIFFRACTIONf_dihedral_angle_d20.986439
X-RAY DIFFRACTIONf_chiral_restr0.085198
X-RAY DIFFRACTIONf_plane_restr0.008224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.7640.2811190.21282258X-RAY DIFFRACTION87
1.764-1.90010.22661330.18892540X-RAY DIFFRACTION98
1.9001-2.09130.24081350.16962554X-RAY DIFFRACTION98
2.0913-2.39380.20911370.16062609X-RAY DIFFRACTION99
2.3938-3.01540.20851390.1662643X-RAY DIFFRACTION99
3.0154-29.11940.19071500.15072824X-RAY DIFFRACTION98
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)
15.33535.13750.43884.96240.65855.1179-0.27590.0884-0.5118-0.13010.1936-0.24010.5015-0.02110.05870.30730.02330.01380.20810.01870.3739-14.03510.4361-3.3102
23.2982-0.65250.14853.1262-0.82143.18760.02780.28190.1495-0.101-0.0603-0.1336-0.09130.07170.04460.1649-0.02070.02230.1964-0.01760.1863-16.696717.9453-7.8604
37.01360.5930.37062.1689-0.12522.47710.04120.5129-0.0392-0.1124-0.08490.16630.0169-0.22550.02020.171-0.0110.00880.2598-0.06150.1587-23.030310.6269-15.123
47.4512.5031-3.84835.3869-2.15262.15050.76581.6535-0.9498-2.46580.4933-1.76281.73742.4188-1.07760.81260.10370.1050.8641-0.29650.5902-7.24382.4276-13.844
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 10:29)
2X-RAY DIFFRACTION2(chain A and resid 30:111)
3X-RAY DIFFRACTION3(chain A and resid 112:164)
4X-RAY DIFFRACTION4(chain A and resid 165:169)

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