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- PDB-4mkm: Repeat domains 1 & 2 of Clostridium perfringens Cpe0147 -

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Basic information

Entry
Database: PDB / ID: 4mkm
TitleRepeat domains 1 & 2 of Clostridium perfringens Cpe0147
ComponentsPutative surface anchored protein
KeywordsUNKNOWN FUNCTION / IgG-like fold / internal ester crosslink
Function / homology
Function and homology information


membrane / metal ion binding
Similarity search - Function
Immunoglobulin-like - #3930 / T-Q ester bond containing domain / T-Q ester bond containing domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / Immunoglobulin-like ...Immunoglobulin-like - #3930 / T-Q ester bond containing domain / T-Q ester bond containing domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Putative surface anchored protein
Similarity search - Component
Biological speciesClostridium perfringens B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsKwon, H. / Squire, C.J. / Young, P.G. / Baker, E.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Autocatalytically generated Thr-Gln ester bond cross-links stabilize the repetitive Ig-domain shaft of a bacterial cell surface adhesin.
Authors: Kwon, H. / Squire, C.J. / Young, P.G. / Baker, E.N.
History
DepositionSep 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Feb 12, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative surface anchored protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8095
Polymers38,6491
Non-polymers1604
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.188, 63.448, 104.984
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 surface anchored protein


Mass: 38648.785 Da / Num. of mol.: 1 / Fragment: domain 1 and domain 2, UNP residues 292-625
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens B (bacteria) / Strain: ATCC 3626 / Gene: AC1_0147 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1R775
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12.5% PEG1000, 12.5% PEG 3350, 12.5% MPD, 0.03 M MgCl2, 0.03 M CaCl2- and 0.1 M bicine/Trizma base pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2012
RadiationMonochromator: unknown / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→19.62 Å / Num. all: 33221 / Num. obs: 33221 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Biso Wilson estimate: 38.31 Å2 / Net I/σ(I): 16.9
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 14.6 % / Num. unique all: 4751 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→19.62 Å / Cor.coef. Fo:Fc: 0.9536 / Cor.coef. Fo:Fc free: 0.9491 / SU R Cruickshank DPI: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 1567 5.02 %RANDOM
Rwork0.1993 ---
all0.2009 31186 --
obs0.2009 31186 93.96 %-
Displacement parametersBiso mean: 46.02 Å2
Baniso -1Baniso -2Baniso -3
1--5.7353 Å20 Å20 Å2
2--3.7634 Å20 Å2
3---1.9719 Å2
Refine analyzeLuzzati coordinate error obs: 0.459 Å
Refinement stepCycle: LAST / Resolution: 1.75→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 4 238 2471
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014481HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.248118HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1037SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes658HARMONIC5
X-RAY DIFFRACTIONt_it4481HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion16.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion309SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4899SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.81 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.5136 46 3.77 %
Rwork0.4061 1174 -
all0.4099 1220 -
obs--93.96 %
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)
10.7763-0.5176-1.00781.7809-0.41065.33130.01460.1632-0.03060.06330.07960.0368-0.1258-0.4123-0.0941-0.0965-0.01990.0309-0.00330.0114-0.1101-0.5791-30.431738.2981
20.9058-0.44090.73412.7542-0.40332.93930.1713-0.0055-0.0526-0.1783-0.02540.17990.2848-0.0595-0.14590.04560.0198-0.0712-0.1152-0.0016-0.148-0.3807-17.6054-20.9181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 148}A1 - 148
2X-RAY DIFFRACTION2{A|149 - 292}A149 - 292

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