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- PDB-3lso: Crystal structure of Putative membrane anchored protein from Cory... -

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Basic information

Entry
Database: PDB / ID: 3lso
TitleCrystal structure of Putative membrane anchored protein from Corynebacterium diphtheriae
Components(Putative membrane anchored protein) x 2
KeywordsMEMBRANE PROTEIN / MCSG / Corynebacterium diphtheriae / PSI-2 / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Immunoglobulin-like - #2260 / Immunoglobulin-like - #2270 / Bacterial Ig-like domain (group 3) / Bacterial Ig-like domain (group 3) / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative membrane anchored protein
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsChang, C. / Sather, A. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Putative membrane anchored protein from Corynebacterium diphtheriae
Authors: Chang, C. / Sather, A. / Clancy, S. / Joachimiak, A.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative membrane anchored protein
B: Putative membrane anchored protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6103
Polymers104,5752
Non-polymers351
Water1,11762
1
A: Putative membrane anchored protein


Theoretical massNumber of molelcules
Total (without water)52,2871
Polymers52,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative membrane anchored protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3232
Polymers52,2871
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.205, 95.517, 160.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative membrane anchored protein


Mass: 52287.340 Da / Num. of mol.: 1 / Fragment: sequence database residues 23-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: DIP2116 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q6NEZ3
#2: Protein Putative membrane anchored protein


Mass: 52287.340 Da / Num. of mol.: 1 / Fragment: sequence database residues 23-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: DIP2116 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q6NEZ3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% PEG 8000, 0.1M citrate-phosphate pH 4.2, 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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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 17, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 30162 / Num. obs: 30141 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 27.4
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3 / Num. unique all: 1485 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.909 / SU B: 30.749 / SU ML: 0.28 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.122 / ESU R Free: 0.339
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25107 1521 5.1 %RANDOM
Rwork0.21459 ---
all0.2165 30054 --
obs0.2165 30054 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.517 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å20 Å2
2--0.32 Å20 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6594 0 1 62 6657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226726
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9759175
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3265888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86326.169248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.361151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6671513
X-RAY DIFFRACTIONr_chiral_restr0.0890.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215035
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5281.54447
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00227206
X-RAY DIFFRACTIONr_scbond_it1.44132279
X-RAY DIFFRACTIONr_scangle_it2.5444.51969
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.747→2.818 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 113 -
Rwork0.311 2051 -
obs-2164 99.77 %
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)
11.6287-0.3602-2.67421.3514-1.302114.19330.1399-0.37610.1994-0.2262-0.0593-0.0068-0.94160.3162-0.08060.2762-0.058-0.02580.2663-0.01650.304220.684415.318744.9748
23.73140.26423.67872.5066-0.29887.81160.22890.2737-0.3556-0.0047-0.0049-0.00190.58440.041-0.2240.15010.02790.00750.043-0.03330.190710.51551.591591.1955
32.2755-1.1284-0.29967.8072.89765.6881-0.2204-0.1307-0.22771.27080.3877-0.38530.38580.4426-0.16730.29670.0813-0.15350.0932-0.01540.174225.420220.5626120.569
46.98121.88924.0531-0.18090.44061.69280.11222.0242-1.6623-0.11980.941-0.97580.01541.661-1.05320.52590.3153-0.07311.1852-0.80130.927323.8378-2.489691.9214
51.895-0.0834-0.87542.4557-2.022211.89040.1202-0.09990.32810.3160.08350.1515-0.6305-0.6215-0.20370.359-0.14720.03030.1336-0.01240.122749.840613.5064-1.3479
64.84960.20840.85796.62412.345511.203-0.2210.0087-0.1786-0.80630.18310.36930.8161-0.69550.03780.401-0.0994-0.04140.06010.00360.079349.282-1.705245.3123
73.7741-1.5887-0.70642.23990.80532.71820.06040.1828-0.0632-0.0869-0.0688-0.02540.0942-0.05040.00840.0252-0.0354-0.03150.15280.00270.183544.075121.800774.0978
80.9019-3.1946-4.93989.505914.532720.85440.60040.29640.2924-0.60960.035-0.8813-0.6578-0.431-0.63541.00350.11420.31510.8475-0.25760.688561.9813.611149.2437
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 211
2X-RAY DIFFRACTION2A212 - 306
3X-RAY DIFFRACTION3A307 - 470
4X-RAY DIFFRACTION4A471 - 487
5X-RAY DIFFRACTION5B44 - 211
6X-RAY DIFFRACTION6B212 - 306
7X-RAY DIFFRACTION7B307 - 470
8X-RAY DIFFRACTION8B471 - 487

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