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- PDB-3lkv: Crystal structure of conserved domain protein from vibrio cholera... -

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Basic information

Entry
Database: PDB / ID: 3lkv
TitleCrystal structure of conserved domain protein from vibrio cholerae o1 biovar eltor str. n16961
Componentsuncharacterized CONSERVED DOMAIN PROTEIN
KeywordsATP binding protein / ATPase Binding Cassette / PSI / MCSG / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


ABC transporter, substrate-binding protein / ABC transporter substrate binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHENYLALANINE / Uncharacterized protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsNocek, B. / Duggan, E. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of conserved domain protein from vibrio cholerae o1 biovar eltor str. n16961
Authors: Nocek, B. / Duggan, E. / Abdullah, J. / Joachimiak, A.
History
DepositionJan 27, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionMar 2, 2010ID: 2QH8
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized CONSERVED DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1767
Polymers31,6271
Non-polymers5506
Water2,000111
1
A: uncharacterized CONSERVED DOMAIN PROTEIN
hetero molecules

A: uncharacterized CONSERVED DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,35214
Polymers63,2532
Non-polymers1,09912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_564z+1/4,-y+5/4,x-1/41
Buried area2670 Å2
ΔGint-260 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.256, 144.256, 144.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Detailsunknown

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Components

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Protein , 1 types, 1 molecules A

#1: Protein uncharacterized CONSERVED DOMAIN PROTEIN


Mass: 31626.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar El Tor str. N16961 / Gene: VC_1101 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q9KT04

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Non-polymers , 5 types, 117 molecules

#2: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.93 Å3/Da / Density % sol: 68.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 550 MME 0.01M ZINC SULFATE 0.1M BIS-TRIS PH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97970, 0.97950, 1.28000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2007 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97951
31.281
ReflectionResolution: 2.2→40 Å / Num. all: 26598 / Num. obs: 26598 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 30 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 30 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 10 / Num. unique all: 1311 / % possible all: 100

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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: MAD / Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.896 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.162 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20339 1268 5.1 %RANDOM
Rwork0.17835 ---
all0.18 25100 --
obs0.17966 23804 94.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.907 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 26 111 2310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222227
X-RAY DIFFRACTIONr_bond_other_d0.0010.021427
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9853022
X-RAY DIFFRACTIONr_angle_other_deg0.9733559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5825295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72126.83579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4215378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.682154
X-RAY DIFFRACTIONr_chiral_restr0.0970.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.921.51476
X-RAY DIFFRACTIONr_mcbond_other0.251.5601
X-RAY DIFFRACTIONr_mcangle_it1.72222374
X-RAY DIFFRACTIONr_scbond_it3.0433751
X-RAY DIFFRACTIONr_scangle_it5.0934.5648
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 107 -
Rwork0.231 1758 -
obs--97.19 %
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)
11.0468-0.23690.23522.00970.11540.8210.00520.00760.04950.15770.0746-0.0041-0.0041-0.0503-0.07980.09390.0006-0.02330.08180.03590.079672.522183.976726.1932
20.9892-1.07650.8161.8725-1.10111.0033-0.00640.02560.0765-0.0146-0.035-0.22610.05310.0480.04140.08310.0017-0.03720.07140.02390.128187.154769.636925.3001
30.4227-0.72460.91431.9648-1.51942.9693-0.05620.19710.28780.3093-0.3021-0.6130.26680.70950.35830.27510.0515-0.12980.28630.04930.3047101.269472.333235.9922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 82
2X-RAY DIFFRACTION2A83 - 265
3X-RAY DIFFRACTION3A266 - 298

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