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- PDB-4kqt: Crystal structure of a putative outer membrane chaperone (OmpH-li... -

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Basic information

Entry
Database: PDB / ID: 4kqt
TitleCrystal structure of a putative outer membrane chaperone (OmpH-like) (CC_1914) from Caulobacter crescentus CB15 at 2.83 A resolution (PSI Community Target, Shapiro)
ComponentsPutative outer membrane chaperone (OmpH-like)
KeywordsCHAPERONE / PF03938 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyChaperone protein Skp / Skp domain superfamily / Outer membrane protein (OmpH-like) / Outer membrane protein (OmpH-like) / unfolded protein binding / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uncharacterized protein
Function and homology information
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.83 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative outer membrane chaperone (OmpH-like) (CC_1914) from Caulobacter crescentus CB15 at 2.83 A resolution (PSI Community Target, Shapiro)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative outer membrane chaperone (OmpH-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0495
Polymers21,5361
Non-polymers5134
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.849, 109.849, 163.704
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Putative outer membrane chaperone (OmpH-like)


Mass: 21535.914 Da / Num. of mol.: 1 / Fragment: UNP residues 37-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: ATCC 19089 / CB15 / Gene: CC_1914 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9A712
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (37-212) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 4.41 Å3/Da / Density % sol: 72.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.20M sodium chloride, 40.00% polyethylene glycol 400, 0.1M Na/K phosphate pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97917,0.91837,0.97862
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979171
20.918371
30.978621
ReflectionResolution: 2.83→45.677 Å / Num. obs: 9290 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 90.539 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.65
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.83-2.930.9461.95054903199.8
2.93-3.050.6872.44935934199.6
3.05-3.190.3954.25041913199.7
3.19-3.350.2785.95119886199.9
3.35-3.560.1591052659191100
3.56-3.840.09915.45264946199.9
3.84-4.220.06721.14851919199.5
4.22-4.820.0492952719131100
4.82-6.050.04927.44997948199.7
6.05-45.6770.02545.652661008199.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.83→45.677 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 27.679 / SU ML: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.371 / ESU R Free: 0.275
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. PEG MODELED IS PRESENT IN CRYO/CRYSTALLIZATION CONDITIONS. 5. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 6. ZERO-OCCUPANCY ATOMS WERE PLACED NEAR THE THREE-FOLD AXIS TO EXCLUDE SOLVENT MASK NEAR THIS REGION. 7. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 441 4.7 %RANDOM
Rwork0.2084 ---
obs0.2101 8849 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.79 Å2 / Biso mean: 85.6935 Å2 / Biso min: 60.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å22.93 Å2-0 Å2
2--2.93 Å2-0 Å2
3----9.5 Å2
Refinement stepCycle: LAST / Resolution: 2.83→45.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 34 4 1334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221346
X-RAY DIFFRACTIONr_bond_other_d0.0020.021350
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.9771809
X-RAY DIFFRACTIONr_angle_other_deg0.70233095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1235170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6625.48462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07115240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1971510
X-RAY DIFFRACTIONr_chiral_restr0.0520.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
X-RAY DIFFRACTIONr_mcbond_it2.5817.067677
X-RAY DIFFRACTIONr_mcbond_other2.5077.059676
X-RAY DIFFRACTIONr_mcangle_it4.16110.587845
LS refinement shellResolution: 2.83→2.904 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 26 -
Rwork0.357 660 -
all-686 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 18.8879 Å / Origin y: 69.0939 Å / Origin z: 63.7845 Å
111213212223313233
T0.0699 Å2-0.0302 Å20.0014 Å2-0.0656 Å2-0.0523 Å2--0.1457 Å2
L0.534 °20.1527 °2-0.8475 °2-0.1805 °2-0.2228 °2--2.2485 °2
S-0.0693 Å °-0.042 Å °0.0065 Å °-0.0289 Å °0.0331 Å °-0.0474 Å °-0.04 Å °0.0373 Å °0.0362 Å °

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