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- PDB-4rho: Crystal structure of a hypothetical protein (BPSL2088) from Burkh... -

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Basic information

Entry
Database: PDB / ID: 4rho
TitleCrystal structure of a hypothetical protein (BPSL2088) from Burkholderia pseudomallei K96243 at 2.25 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / New fold / six stranded anit-parallel sheet surrounded by alpha-helices / Imm32 Pfam family / PF15579 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyImm52 family, TsiT-like / Immunity protein 52 / Immunity protein 52 / TRIETHYLENE GLYCOL / Imm52 domain-containing protein
Function and homology information
Biological speciesBurkholderia pseudomallei K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BPSL2088) from Burkholderia pseudomallei K96243 at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9114
Polymers57,6112
Non-polymers3002
Water1,874104
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9562
Polymers28,8051
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9562
Polymers28,8051
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.344, 85.704, 156.285
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 28805.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria)
Strain: K96243 / Gene: BPSL2088 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q63T80
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE THE CONSTRUCT (1-240) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 30.0% PEG-6000, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97937,0.97895
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 3, 2007
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979371
30.978951
ReflectionResolution: 2.25→39.071 Å / Num. obs: 24536 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.632 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 6.87
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.25-2.330.5492.278682385197.6
2.33-2.420.4932.683692295199.7
2.42-2.530.4322.889232455199.6
2.53-2.670.3193.893772566199.6
2.67-2.830.2684.484432309199.5
2.83-3.050.1875.688592446199.2
3.05-3.360.1327.689582492199.4
3.36-3.840.08110.885742429199.2
3.84-4.830.05813.687552494198.6
4.83-39.0710.05314.190162665197.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.25→39.071 Å / Cor.coef. Fo:Fc: 0.9355 / Cor.coef. Fo:Fc free: 0.9254 / Occupancy max: 1 / Occupancy min: 0.33 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5.A POLYETHYLENE GLYCOL FRAGMENTS (PGE) WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 1247 5.09 %RANDOM
Rwork0.2238 ---
obs0.225 24486 99.09 %-
Displacement parametersBiso max: 108.76 Å2 / Biso mean: 41.2353 Å2 / Biso min: 11.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.6442 Å20 Å20 Å2
2---3.5883 Å20 Å2
3---0.9442 Å2
Refine analyzeLuzzati coordinate error obs: 0.379 Å
Refinement stepCycle: LAST / Resolution: 2.25→39.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3918 0 17 104 4039
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1881SINUSOIDAL10
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes606HARMONIC5
X-RAY DIFFRACTIONt_it4077HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion542SEMIHARMONIC5
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_contact4764SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4077HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5560HARMONIC100.34
X-RAY DIFFRACTIONt_omega_torsion3.68
X-RAY DIFFRACTIONt_other_torsion1.89
LS refinement shellResolution: 2.25→2.35 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.246 152 5.2 %
Rwork0.2166 2771 -
all0.2181 2923 -
obs--99.09 %
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)
11.1278-0.42380.78330.9627-0.91732.52150.00640.02510.1063-0.0646-0.0496-0.0073-0.14010.12540.0432-0.1842-0.0248-0.01030.2074-0.026-0.19289.30983.371835.2893
20.96650.2619-0.54121.0693-0.68421.68990.0263-0.0713-0.0220.0498-0.03860.0220.11910.08030.0123-0.17250.01130.00210.2193-0.0131-0.18128.3651-3.33263.4789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-15 - 240
2X-RAY DIFFRACTION2B-16 - 240

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