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- PDB-3elg: Crystal structure of a putative periplasmic protein of unknown fu... -

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Basic information

Entry
Database: PDB / ID: 3elg
TitleCrystal structure of a putative periplasmic protein of unknown function (bvu_2443) from bacteroides vulgatus atcc 8482 at 1.64 A resolution
Componentsuncharacterized periplasmic protein
KeywordsMEMBRANE PROTEIN / Blip-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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 / CITRIC ACID / Putative beta-lactamase-inhibitor-like PepSY-like domain-containing protein
Function and homology information
Biological speciesBacteroides vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.64 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of putative periplasmic protein of unknown function (YP_001299723.1) from Bacteroides vulgatus ATCC 8482 at 1.64 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized periplasmic protein
B: uncharacterized periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3853
Polymers29,1932
Non-polymers1921
Water6,089338
1
A: uncharacterized periplasmic protein


Theoretical massNumber of molelcules
Total (without water)14,5961
Polymers14,5961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7882
Polymers14,5961
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.242, 73.507, 53.544
Angle α, β, γ (deg.)90.000, 108.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein uncharacterized periplasmic protein


Mass: 14596.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria)
Gene: YP_001299723.1, BVU_2443 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6L337
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE THE CONSTRUCT (RESIDUES 20-146) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...SEQUENCE THE CONSTRUCT (RESIDUES 20-146) 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 23.8% polyethylene glycol 3000, 0.1M citric acid pH 6.0, 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: 0.97864
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 7, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 1.64→29.775 Å / Num. obs: 35714 / % possible obs: 98.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 20.084 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 5.959
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.64-1.683.80.8650.91004426210.86597.2
1.68-1.7370.7910.91777325220.79197.3
1.73-1.787.70.6381.21892524680.63897.3
1.78-1.837.70.4711.61838323970.47197.9
1.83-1.897.70.3721790023330.3798
1.89-1.967.70.2862.61736922680.28697.8
1.96-2.037.70.2113.61688522030.21198.4
2.03-2.127.70.18241617921120.18298.4
2.12-2.217.70.1395.31568720400.13998.5
2.21-2.327.60.135.31476719310.1398.6
2.32-2.447.70.1116.61412318410.11199
2.44-2.597.70.0987.31347317530.09898.9
2.59-2.777.70.097.51269016560.0999.1
2.77-2.997.60.07791188615550.07799.2
2.99-3.287.70.06510.21085014180.06599.5
3.28-3.677.60.05811.3991213030.05899.5
3.67-4.237.60.05611.2863811350.05699.7
4.23-5.197.50.04812.773509760.04899.7
5.19-7.337.40.0610.956497600.0699.7
7.33-29.87.10.05611.730144220.05697.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0069refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.64→29.775 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.741 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.097
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (4). ONE CITRATE (CIT) ION WAS MODELED BASED ON CRYSTALLIZATION AND CONCLUSIVE ELECTRON DENSITY. (5). RAMACHANDRAN OUTLIERS OF LYS 87 IN BOTH A AND B SUBUNITS ARE SUPPORTED BY ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1784 5 %RANDOM
Rwork0.172 ---
obs0.174 35686 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.67 Å2 / Biso mean: 22.186 Å2 / Biso min: 8.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20.5 Å2
2--0.08 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.64→29.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 13 338 2352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222302
X-RAY DIFFRACTIONr_bond_other_d0.0020.021558
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9673143
X-RAY DIFFRACTIONr_angle_other_deg1.40133847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5265305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12325.727110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72315426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.609158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022717
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02461
X-RAY DIFFRACTIONr_mcbond_it1.77431415
X-RAY DIFFRACTIONr_mcbond_other0.5463570
X-RAY DIFFRACTIONr_mcangle_it2.93852322
X-RAY DIFFRACTIONr_scbond_it4.9478887
X-RAY DIFFRACTIONr_scangle_it7.51811821
LS refinement shellResolution: 1.639→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 136 -
Rwork0.259 2473 -
all-2609 -
obs--96.77 %
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)
10.7683-0.6482-0.31431.31050.31450.914-0.0354-0.0237-0.02460.0008-0.00740.0102-0.00130.08750.0428-0.0431-0.0031-0.013-0.028-0.0001-0.03159.999510.20548.9038
20.87990.5101-0.00730.8124-0.58940.89210.09210.01050.06340.0248-0.0897-0.0774-0.04810.0426-0.0023-0.00860.00810.0231-0.0370.0079-0.019-1.68938.2553-13.1102
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 146
2X-RAY DIFFRACTION2B21 - 146

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