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- PDB-4r7r: Crystal Structure of Putative Lipoprotein from Clostridium perfringens -

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Basic information

Entry
Database: PDB / ID: 4r7r
TitleCrystal Structure of Putative Lipoprotein from Clostridium perfringens
ComponentsPutative lipoprotein
KeywordsLIPID BINDING PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-fold
Function / homologyUncharacterised protein PF16224, DUF4883 / Protein of unknown function DUF4883 / DOmain of unknown function (DUF4883) / Dna Ligase; domain 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta / Putative lipoprotein / Putative lipoprotein
Function and homology information
Biological speciesClostridium perfringens ATCC 13124 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.449 Å
AuthorsKim, Y. / Zhou, M. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Putative Lipoprotein from Clostridium perfringens
Authors: Kim, Y. / Zhou, M. / Shatsman, S. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2092
Polymers15,1171
Non-polymers921
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.743, 58.743, 85.984
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative lipoprotein


Mass: 15117.034 Da / Num. of mol.: 1 / Fragment: d30 / Mutation: N-terminal deletion (1-30)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens ATCC 13124 (bacteria)
Strain: ATCC 13124 / Gene: CPF_1278 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q0TRL6, UniProt: A0A0H2YS77*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris 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-BM / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 28, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.449→50 Å / Num. all: 6691 / Num. obs: 6691 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 32.89 Å2 / Rsym value: 0.116 / Net I/σ(I): 13.9
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 310 / Rsym value: 0.659 / % possible all: 99

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.449→32.837 Å / SU ML: 0.23 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.238 314 5.12 %random
Rwork0.185 ---
all0.188 6137 --
obs0.188 6137 92.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.9 Å2
Refinement stepCycle: LAST / Resolution: 2.449→32.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 6 33 1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091038
X-RAY DIFFRACTIONf_angle_d1.1011404
X-RAY DIFFRACTIONf_dihedral_angle_d13.415396
X-RAY DIFFRACTIONf_chiral_restr0.04159
X-RAY DIFFRACTIONf_plane_restr0.004177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4494-3.08560.27881390.21382610274984
3.0856-32.83970.22391750.174932133388100
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)
16.7645-0.2954-7.37846.9411-0.90258.2634-0.50972.3429-0.8271-1.17980.1599-0.30151.10290.1040.19480.36210.04240.15840.8995-0.10870.473237.5448-21.4806-27.67
28.9657-3.8865-2.47895.33565.14265.43940.41130.94981.1471-0.80130.3765-0.7758-0.99450.8556-0.45950.40070.03370.03740.44870.07660.314529.7047-10.3197-25.9502
35.79650.20960.40177.00980.31364.9816-0.0917-0.45560.0255-0.04810.38140.2678-0.4893-0.5701-0.17620.28210.10330.00320.4229-0.04760.326415.8155-11.6959-12.6158
44.0175-2.78542.51064.0911-4.75415.7665-0.10220.13781.03080.5526-0.4165-0.6011-0.4171-1.08590.29430.40060.01170.11830.4026-0.02060.374517.8346-3.1-9.3184
59.1097-7.2582-1.59727.94691.35464.01460.0483-0.19421.5059-0.222-0.0617-1.0704-0.53990.6067-0.18120.3377-0.02270.04160.3070.05960.242533.6702-8.659-15.0055
66.94952.8287-5.68251.9719-2.93955.1602-1.051.0424-1.6464-1.1320.0397-0.54481.5088-0.31220.23470.5233-0.0562-0.01480.2689-0.17690.330826.1511-25.7857-15.4326
75.79640.6781-0.4056.0862-2.03777.90640.10280.35490.3822-0.74910.1894-0.3689-0.6001-0.5994-0.22560.37480.03460.10090.239-0.03710.338418.9879-9.7579-19.3726
82.37151.6486-0.93952.13151.32914.77910.12460.0923-0.03870.11050.0419-0.07350.3020.2893-0.10090.2050.0473-0.03410.1813-0.00710.230126.9429-17.4498-16.4591
95.56980.27940.15283.6826-0.74244.6286-0.0892-0.0269-0.13210.60620.01110.48190.274-1.03320.12440.25680.00050.02380.3361-0.02640.213721.4711-10.4393-3.7494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 15 )
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 31 )
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 39 )
5X-RAY DIFFRACTION5chain 'A' and (resid 40 through 54 )
6X-RAY DIFFRACTION6chain 'A' and (resid 55 through 66 )
7X-RAY DIFFRACTION7chain 'A' and (resid 67 through 76 )
8X-RAY DIFFRACTION8chain 'A' and (resid 77 through 112 )
9X-RAY DIFFRACTION9chain 'A' and (resid 113 through 123 )

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