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- PDB-4l7a: Crystal structure of a putative zinc-binding metallo-peptidase (B... -

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Basic information

Entry
Database: PDB / ID: 4l7a
TitleCrystal structure of a putative zinc-binding metallo-peptidase (BACCAC_01431) from Bacteroides caccae ATCC 43185 at 2.10 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Putative zinc-binding metallo-peptidase / PF15890 family protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyCollagenase (Catalytic Domain) - #70 / Substrate import-associated zinc metallohydrolase lipoprotein / Putative zinc-binding metallo-peptidase / Collagenase (Catalytic Domain) / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACCAC_01431) from Bacteroides caccae ATCC 43185 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: 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 1.3Feb 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: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)63,4132
Polymers63,4132
Non-polymers00
Water5,981332
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)31,7071
Polymers31,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)31,7071
Polymers31,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-8 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.096, 116.117, 135.823
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: 31706.721 Da / Num. of mol.: 2 / Fragment: UNP residues 28-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae (bacteria) / Gene: BACCAC_01431 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5ZEW7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (28-297) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (28-297) 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 30.00% polyethylene glycol 3000, 0.01M EDTA sodium salt, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979284
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979284 Å / Relative weight: 1
ReflectionResolution: 2.09→29.59 Å / Num. obs: 37077 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.33 Å2 / Rmerge(I) obs: 0.187 / Net I/σ(I): 7.57
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.0946-2.161.072408065678184.9
2.16-2.250.8492.6561297298199.5
2.25-2.350.7083.1533556928199.6
2.35-2.480.5244573637421199.8
2.48-2.630.4184.9527386826199.8
2.63-2.830.3096.3541567017199.8
2.83-3.120.2078.75522371851100
3.12-3.570.13812538217104199.8
3.57-4.490.010315526577028199.8
4.49-29.590.08316538247125199.4

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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
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→29.59 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.451 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.182
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. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 5. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 1853 5 %RANDOM
Rwork0.2025 ---
obs0.2041 37017 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.43 Å2 / Biso mean: 29.1869 Å2 / Biso min: 13.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---1.22 Å2-0 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.09→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 0 332 4576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224434
X-RAY DIFFRACTIONr_bond_other_d0.0040.024119
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9446039
X-RAY DIFFRACTIONr_angle_other_deg0.97439520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4445543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94124.537216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53815766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.571518
X-RAY DIFFRACTIONr_chiral_restr0.0960.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025009
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021017
X-RAY DIFFRACTIONr_mcbond_it1.5632.0422106
X-RAY DIFFRACTIONr_mcbond_other1.5632.0422105
X-RAY DIFFRACTIONr_mcangle_it2.3363.0542635
LS refinement shellResolution: 2.095→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 134 -
Rwork0.248 2326 -
all-2460 -
obs--89.91 %
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)
10.4096-0.2047-0.17140.98970.34860.8794-0.01170.0728-0.0222-0.0348-0.02990.0331-0.0606-0.00250.04160.0079-0.00540.00590.0416-0.0210.04687.208798.127617.084
20.4240.21060.13431.51350.5471.04810.0059-0.09590.00120.103-0.0593-0.06840.06970.010.05350.0096-0.0001-0.00450.0427-0.01510.03577.044299.616351.4665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 297
2X-RAY DIFFRACTION2B38 - 297

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