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- PDB-3c8i: Crystal structure of a putative membrane protein from Corynebacte... -

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Basic information

Entry
Database: PDB / ID: 3c8i
TitleCrystal structure of a putative membrane protein from Corynebacterium diphtheriae
ComponentsPutative membrane protein
KeywordsMEMBRANE PROTEIN / putative membrane protein / Corynebacterium diphtheriae / Structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyputative membrane protein from Corynebacterium diphtheriae fold / putative membrane protein from Corynebacterium diphtheriae superfamily / Protein of unknown function DUF3239 / DUF3239 domain superfamily / Protein of unknown function (DUF3239) / Beta Barrel / Mainly Beta / membrane / Membrane protein
Function and homology information
Biological speciesCorynebacterium diphtheriae NCTC 13129 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsZhang, R. / Hatzos, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a putative membrane protein from Corynebacterium diphtheriae.
Authors: Zhang, R. / Hatzos, C. / Clancy, S. / Joachimiak, A.
History
DepositionFeb 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Putative membrane protein
B: Putative membrane protein


Theoretical massNumber of molelcules
Total (without water)31,0912
Polymers31,0912
Non-polymers00
Water3,171176
1
A: Putative membrane protein
B: Putative membrane protein

A: Putative membrane protein
B: Putative membrane protein


Theoretical massNumber of molelcules
Total (without water)62,1824
Polymers62,1824
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.374, 99.837, 124.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative membrane protein


Mass: 15545.565 Da / Num. of mol.: 2 / Fragment: Residues 75-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae NCTC 13129 (bacteria)
Species: Corynebacterium diphtheriae / Strain: NCTC 13129 / Biotype gravis / Gene: GI:38199630, DIP0771 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6NIK4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M Calcium chloride dihydrate, 0.1M Bis-Tris, 30% v/v PEG MME 550, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→62.26 Å / Num. all: 22137 / Num. obs: 22035 / % possible obs: 99.54 % / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Biso Wilson estimate: 28.01 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 40.13
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2.31 / Num. unique all: 1702 / % possible all: 99.94

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→62.26 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.735 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.159 / ESU R Free: 0.144
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23164 1193 5.1 %RANDOM
Rwork0.20021 ---
all0.20185 22035 --
obs0.20185 22035 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.602 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.95→62.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 176 2146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222009
X-RAY DIFFRACTIONr_bond_other_d0.0010.021334
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9652755
X-RAY DIFFRACTIONr_angle_other_deg0.95633282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.165254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07424.75682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78115332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7431516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02350
X-RAY DIFFRACTIONr_nbd_refined0.2180.2386
X-RAY DIFFRACTIONr_nbd_other0.20.21367
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2955
X-RAY DIFFRACTIONr_nbtor_other0.0880.21087
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2129
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0920.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.210
X-RAY DIFFRACTIONr_mcbond_it1.2891.51675
X-RAY DIFFRACTIONr_mcbond_other0.2141.5498
X-RAY DIFFRACTIONr_mcangle_it1.50422120
X-RAY DIFFRACTIONr_scbond_it2.1763819
X-RAY DIFFRACTIONr_scangle_it3.2484.5635
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 96 -
Rwork0.271 1605 -
obs-1702 99.94 %
Refinement TLS params.Method: refined / Origin x: -1.318 Å / Origin y: 18.336 Å / Origin z: 16.523 Å
111213212223313233
T-0.076 Å20.0052 Å2-0.05 Å2--0.1026 Å2-0.0037 Å2---0.0983 Å2
L1.0361 °2-0.6011 °2-0.7901 °2-2.174 °20.7546 °2--1.9438 °2
S0.0482 Å °0.0721 Å °0.1164 Å °-0.0504 Å °0.0987 Å °-0.1751 Å °-0.1698 Å °-0.0053 Å °-0.147 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 5015 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 141101 - 141
4X-RAY DIFFRACTION1BB13 - 5013 - 50
5X-RAY DIFFRACTION1BB51 - 10051 - 100
6X-RAY DIFFRACTION1BB101 - 141101 - 141

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