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- PDB-5bxg: Crystal structure of an uncharacterized beta-sandwich protein (CD... -

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Basic information

Entry
Database: PDB / ID: 5bxg
TitleCrystal structure of an uncharacterized beta-sandwich protein (CD630_09570) from Clostridium difficile 630 at 1.90 A resolution
Componentsuncharacterized beta-sandwich protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyImmunoprotective extracellular, immunoglobulin-like domain superfamily / Putative phage lipoprotein
Function and homology information
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an uncharacterized beta-sandwich protein (CD630_09570) from Clostridium difficile 630 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized beta-sandwich protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7634
Polymers18,5761
Non-polymers1863
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.108, 69.108, 87.802
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein uncharacterized beta-sandwich protein


Mass: 18576.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Strain: 630
Gene: CD630_09570, CD630_29070, CDIF630_03179, YP_001087438.1
Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q183Z1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (26-186) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (26-186) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% polyethylene glycol 3350, 0.2M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2015
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.9→49.453 Å / Num. obs: 18773 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.253 % / Biso Wilson estimate: 32.52 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.071 / Net I/σ(I): 15.17 / Num. measured all: 117394
Reflection shell
Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
1.9-1.970.6890.6151.76442194519090.73198.1
1.97-2.050.8940.4923.311871187618740.53699.9
2.05-2.140.9450.3414.912021179717930.3799.8
2.14-2.250.9780.2277.212659183018300.245100
2.25-2.390.9850.1679.612579187718770.181100
2.39-2.580.990.13211.912376191319130.143100
2.58-2.840.9950.09517.313042188418840.103100
2.84-3.250.9970.06224.711981187518730.06899.9
3.25-4.080.9980.04633.212297188718830.0599.8
4.08-49.4530.9990.0436.812126194319370.04499.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
XDSNovember 3, 2014 BUILT=20141118data scaling
XSCALEdata scaling
SHELXphasing
SHARPphasing
SHELXDphasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: SAD / Resolution: 1.9→49.453 Å / Cor.coef. Fo:Fc: 0.9618 / Cor.coef. Fo:Fc free: 0.9525 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1891 960 5.13 %RANDOM
Rwork0.1651 ---
obs0.1663 18713 99.71 %-
Displacement parametersBiso max: 106.92 Å2 / Biso mean: 39.6601 Å2 / Biso min: 22.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.9933 Å20 Å20 Å2
2---1.9933 Å20 Å2
3---3.9866 Å2
Refine analyzeLuzzati coordinate error obs: 0.206 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 12 243 1472
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d628SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes181HARMONIC5
X-RAY DIFFRACTIONt_it1290HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion179SEMIHARMONIC5
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_contact1582SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1290HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1748HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion4.75
X-RAY DIFFRACTIONt_other_torsion2.7
LS refinement shellResolution: 1.9→2.02 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2444 141 4.74 %
Rwork0.2047 2834 -
all0.2066 2975 -
obs--99.71 %
Refinement TLS params.Method: refined / Origin x: 24.6207 Å / Origin y: 25.4638 Å / Origin z: 4.6174 Å
111213212223313233
T-0.0314 Å2-0.0091 Å2-0.0242 Å2--0.0413 Å20.0279 Å2---0.0387 Å2
L1.0361 °2-0.637 °20.4104 °2-0.8573 °2-0.249 °2--1.103 °2
S0.0823 Å °-0.078 Å °-0.0151 Å °-0.1005 Å °0.0482 Å °0.0744 Å °0.0173 Å °-0.0644 Å °-0.1305 Å °
Refinement TLS groupSelection details: {A|36 - 186}

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