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- PDB-4h3w: Crystal structure of a putative secreted protein (BDI_1231) from ... -

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Basic information

Entry
Database: PDB / ID: 4h3w
TitleCrystal structure of a putative secreted protein (BDI_1231) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / two beta barrel domains / secreted protein / ORFan / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyJelly Rolls - #1260 / Protein of unknown function (DUF4621), C-terminal domain / Protein of unknown function DUF4621 / Protein of unknown function (DUF4621) / Hypothetical Protein Tm1070; Chain: A / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BDI_1231) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)74,8062
Polymers74,8062
Non-polymers00
Water7,080393
1
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)37,4031
Polymers37,4031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)37,4031
Polymers37,4031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.746, 65.323, 78.756
Angle α, β, γ (deg.)91.640, 92.350, 104.500
Int Tables number1
Space group name H-MP1

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Components

#1: Protein hypothetical protein /


Mass: 37402.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_1231, YP_001302614.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LBC8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT (RESIDUES 24-352) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...1. THE CONSTRUCT (RESIDUES 24-352) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30.0% polyethylene glycol 4000, 0.2M magnesium chloride, 0.1M TRIS pH 8.5, 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: 0.97885
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 1.87→48.317 Å / Num. obs: 53817 / % possible obs: 87.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.595 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.87-1.940.571.813764397161.5
1.94-2.010.4212.518617509591.8
2.01-2.110.2713.922778626293
2.11-2.220.2154.820391556992
2.22-2.360.1556.820208556390.1
2.36-2.540.1169.121096570693.5
2.54-2.790.08812.219498533988.1
2.79-3.190.05718.520446557290.5
3.19-4.020.0424.519209528485.3
4.020.03828.419668545687.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
REFMAC5.7.0029refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→48.317 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 7.939 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.155
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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.SOLVENT WAS EXCLUDED FROM TLS REFINEMENT. 4. THE PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO CRYSTALLIZATION LYSINES HAVE BEEN MODELED AS N-DIMETHYL-LYSINE (MLY).5. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 6. THE NOMINAL RESOLUTION IS 2.00 ANGSTROMS WITH 7826 OBSERVED REFLECTIONS BETWEEN 2.00-1.87 (71.2% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 2703 5.1 %RANDOM
Rwork0.1963 ---
obs0.1984 53272 86.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 171.09 Å2 / Biso mean: 42.5108 Å2 / Biso min: 20.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20.85 Å2-0.47 Å2
2--3.15 Å20.1 Å2
3----3.19 Å2
Refinement stepCycle: LAST / Resolution: 1.87→48.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4836 0 0 393 5229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195112
X-RAY DIFFRACTIONr_bond_other_d0.0030.024818
X-RAY DIFFRACTIONr_angle_refined_deg1.4792.0247004
X-RAY DIFFRACTIONr_angle_other_deg0.872311169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90326.278223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16515647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5071513
X-RAY DIFFRACTIONr_chiral_restr0.0450.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215798
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021037
LS refinement shellResolution: 1.872→1.921 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 91 -
Rwork0.449 2185 -
all-2276 -
obs--49.82 %
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)
11.05420.62950.58280.98080.44131.7230.0862-0.00190.07990.0822-0.0289-0.025-0.197-0.085-0.05740.12040.03770.02040.01620.02120.157713.23153.793944.4131
20.7998-0.5499-0.54810.87950.41731.81450.09160.0158-0.0415-0.0781-0.0124-0.04150.2171-0.1386-0.07930.1189-0.0509-0.05060.02620.02520.15339.8578-23.923351.2473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 350
2X-RAY DIFFRACTION2B38 - 349

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