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- PDB-3oi8: The crystal structure of functionally unknown conserved protein d... -

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Basic information

Entry
Database: PDB / ID: 3oi8
TitleThe crystal structure of functionally unknown conserved protein domain from Neisseria meningitidis MC58
ComponentsUncharacterized protein
KeywordsStructural genomics / Unknown function / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


flavin adenine dinucleotide binding / metal ion binding / plasma membrane
Similarity search - Function
CBS domain Like - #20 / CBS domain Like / Transporter-associated domain / Transporter associated domain / Transporter associated domain / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily ...CBS domain Like - #20 / CBS domain Like / Transporter-associated domain / Transporter associated domain / Transporter associated domain / Ion transporter-like, CBS domain / CBS-domain / CBS-domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / DI(HYDROXYETHYL)ETHER / CBS domain-containing protein
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.989 Å
AuthorsZhang, R. / Tan, K. / Li, H. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of functionally unknown conserved protein domain from Neisseria meningitidis MC58
Authors: Zhang, R. / Tan, K. / Li, H. / Cobb, G. / Joachimiak, A.
History
DepositionAug 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 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 protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8146
Polymers36,0822
Non-polymers7334
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-26 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.640, 52.156, 64.010
Angle α, β, γ (deg.)90.00, 112.67, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. It is predicted that the chains A and B form a dimer.

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Components

#1: Protein Uncharacterized protein


Mass: 18040.861 Da / Num. of mol.: 2 / Fragment: sequence database residues 24-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: MC58 / Gene: NMB0537 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q9K0P8
#2: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: 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
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% w/v PEG8000, 0.1M Tris, 0.2M MgCl2, pH 8.5, 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: 0.97926, 0.97942
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.979421
ReflectionResolution: 2→39.1 Å / Num. all: 22323 / Num. obs: 22323 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 25.97 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.07 / % possible all: 72

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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: MAD / Resolution: 1.989→39.095 Å / SU ML: 0.23 / σ(F): 0.03 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1089 5.13 %
Rwork0.1823 --
obs0.185 21239 94.03 %
all-21239 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.3 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.504 Å20 Å2-1.2699 Å2
2--8.3596 Å20 Å2
3----2.8556 Å2
Refinement stepCycle: LAST / Resolution: 1.989→39.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 51 142 2686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072588
X-RAY DIFFRACTIONf_angle_d1.053495
X-RAY DIFFRACTIONf_dihedral_angle_d17.638995
X-RAY DIFFRACTIONf_chiral_restr0.072397
X-RAY DIFFRACTIONf_plane_restr0.004450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9895-2.080.29091080.22592083X-RAY DIFFRACTION79
2.08-2.18960.25481270.19722409X-RAY DIFFRACTION90
2.1896-2.32680.28551060.19152511X-RAY DIFFRACTION93
2.3268-2.50640.28461400.19552520X-RAY DIFFRACTION95
2.5064-2.75860.28571420.20112615X-RAY DIFFRACTION98
2.7586-3.15760.2151440.19182648X-RAY DIFFRACTION99
3.1576-3.97770.19991580.16472666X-RAY DIFFRACTION100
3.9777-39.10230.21081640.1662698X-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)
11.1218-0.1388-0.48220.1606-0.371.7832-0.05080.14460.09780.02840.03850.0027-0.22580.01430.01280.1507-0.0327-0.00540.08950.01420.1392-11.284624.198542.1635
21.3205-0.7058-0.61680.2827-0.43591.6238-0.1410.25680.0077-0.11640.05890.05450.2952-0.08760.02550.1717-0.1004-0.00610.1537-0.00570.0857-29.878926.78641.9203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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