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- PDB-4poi: Crystal structure of a putative periplasmic protein (BACCAC_02096... -

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Basic information

Entry
Database: PDB / ID: 4poi
TitleCrystal structure of a putative periplasmic protein (BACCAC_02096) from Bacteroides caccae ATCC 43185 at 2.30 A resolution
ComponentsPutative periplasmic protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two copies of DUF2874 domain (PF11396) / BLIP-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyInhibitor of vertebrate lysozyme, Ivy - #30 / Putative beta-lactamase-inhibitor-like, PepSY-like / Putative beta-lactamase-inhibitor-like, PepSY-like / Inhibitor of vertebrate lysozyme, Ivy / 3-Layer(aba) Sandwich / Alpha Beta / PepSY_like domain-containing protein
Function and homology information
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative periplasmic protein (BACCAC_02096) from Bacteroides caccae ATCC 43185 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 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

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Assembly

Deposited unit
A: Putative periplasmic protein
B: Putative periplasmic protein


Theoretical massNumber of molelcules
Total (without water)29,3272
Polymers29,3272
Non-polymers00
Water1,838102
1
A: Putative periplasmic protein


Theoretical massNumber of molelcules
Total (without water)14,6631
Polymers14,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative periplasmic protein


Theoretical massNumber of molelcules
Total (without water)14,6631
Polymers14,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.881, 104.881, 56.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative periplasmic protein


Mass: 14663.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae (bacteria) / Strain: ATCC 43185 / Gene: BACCAC_02096 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5ZGS7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 23-150 OF 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 26.0% polyethylene glycol 3350, 0.20M potassium thiocyanate, 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: 0.91837,0.97895
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal 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
20.978951
ReflectionResolution: 2.3→46.904 Å / Num. obs: 14400 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.56 % / Biso Wilson estimate: 46.34 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 38.15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.388.80.2757.4412012135399.9
2.38-2.480.20610.113178148999.9
2.48-2.590.16511.911627137099.9
2.59-2.730.11816.1117961437100
2.73-2.90.08124131081424100
2.9-3.120.05633.8125861400100
3.12-3.430.03550.2126091423100
3.43-3.930.035910988145299
3.93-4.930.02181.212900145899.8
4.93-46.90.02180.212452159498.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMAC5.8.0049refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→46.904 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.944 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.337 / ESU R Free: 0.249
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.2788 722 5 %RANDOM
Rwork0.2436 ---
obs0.2453 14376 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.18 Å2 / Biso mean: 48.7819 Å2 / Biso min: 20.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-0 Å20 Å2
2---0.99 Å2-0 Å2
3---1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 0 102 1980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221928
X-RAY DIFFRACTIONr_bond_other_d0.0040.021856
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9532596
X-RAY DIFFRACTIONr_angle_other_deg1.07134294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0745237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73924.44490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38215353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0481510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212145
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02427
X-RAY DIFFRACTIONr_mcbond_it1.9232.646945
X-RAY DIFFRACTIONr_mcbond_other1.922.643944
X-RAY DIFFRACTIONr_mcangle_it3.0493.9531177
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 52 -
Rwork0.274 990 -
all-1042 -
obs--99.9 %
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)
14.65660.6821-3.08342.06480.28392.34240.04820.06330.13330.06170.05880.02950.0228-0.0079-0.1070.0698-0.0228-0.03850.11310.01260.0299103.832121.039916.395
22.1083-0.216-0.94563.8998-1.38163.23750.0330.30360.50070.0947-0.3691-0.6114-0.29030.13890.33610.0808-0.0046-0.09510.21410.18070.325886.05943.22989.2288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 147
2X-RAY DIFFRACTION2B27 - 148

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