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- PDB-3muq: The crystal structure of a conserved functionally unknown protein... -

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Basic information

Entry
Database: PDB / ID: 3muq
TitleThe crystal structure of a conserved functionally unknown protein from Vibrio parahaemolyticus RIMD 2210633
Componentsuncharacterized conserved protein
Keywordsstructural genomics / unknown function / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyPBP superfamily domain / PBP domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / PBP_domain domain-containing protein
Function and homology information
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.053 Å
AuthorsTan, K. / Wu, R. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a conserved functionally unknown protein from Vibrio parahaemolyticus RIMD 2210633
Authors: Tan, K. / Wu, R. / Bearden, J. / Joachimiak, A.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 protein
B: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)53,5022
Polymers53,5022
Non-polymers00
Water5,531307
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-9 kcal/mol
Surface area19420 Å2
MethodPISA
2
A: uncharacterized conserved protein
B: uncharacterized conserved protein

A: uncharacterized conserved protein
B: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)107,0044
Polymers107,0044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6720 Å2
ΔGint-24 kcal/mol
Surface area37110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.075, 109.088, 51.665
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsExperimentally unknown. The chains A and B may form a dimer.

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Components

#1: Protein uncharacterized conserved protein


Mass: 26750.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VP1501 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q87PK2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.82 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.1M DL-malic acid, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97901 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.05→38 Å / Num. all: 38552 / Num. obs: 38552 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 13.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 1.88 / Num. unique all: 1902 / % 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: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.053→37.509 Å / SU ML: 0.23 / σ(F): 0.03 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 1825 5.06 %random
Rwork0.1642 ---
all0.1663 36083 --
obs0.1663 36083 93.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.348 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7085 Å2-0 Å2-0 Å2
2---2.6441 Å20 Å2
3----1.0644 Å2
Refinement stepCycle: LAST / Resolution: 2.053→37.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 0 307 3973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083760
X-RAY DIFFRACTIONf_angle_d1.0525085
X-RAY DIFFRACTIONf_dihedral_angle_d18.1211373
X-RAY DIFFRACTIONf_chiral_restr0.069539
X-RAY DIFFRACTIONf_plane_restr0.005667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0525-2.12590.26751620.21712943X-RAY DIFFRACTION82
2.1259-2.2110.27871660.20433178X-RAY DIFFRACTION89
2.211-2.31160.23881780.19983218X-RAY DIFFRACTION89
2.3116-2.43340.24841710.18523365X-RAY DIFFRACTION92
2.4334-2.58590.23091980.18143408X-RAY DIFFRACTION94
2.5859-2.78550.21421890.17443435X-RAY DIFFRACTION95
2.7855-3.06570.20262080.16433527X-RAY DIFFRACTION97
3.0657-3.5090.19441860.15843606X-RAY DIFFRACTION98
3.509-4.41980.17351830.12863702X-RAY DIFFRACTION99
4.4198-37.51540.16571840.14683876X-RAY DIFFRACTION99
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)
10.05620.03910.11030.2565-0.07360.4942-0.00290.0442-0.044-0.05410.0187-0.03060.02640.0623-0.00930.0857-0.00250.01720.1045-0.0020.100475.02073.707334.0022
20.8499-0.14590.12790.0381-0.08140.2338-0.0703-0.00250.00150.05410.00230.0147-0.02350.0090.05680.0609-0.01470.00110.0562-0.02110.064362.401220.240250.8228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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