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- PDB-4df9: Crystal structure of a putative peptidase (BF3526) from Bacteroid... -

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Basic information

Entry
Database: PDB / ID: 4df9
TitleCrystal structure of a putative peptidase (BF3526) from Bacteroides fragilis NCTC 9343 at 2.17 A resolution
Componentsputative peptidase
KeywordsHYDROLASE / IgA Peptidase M64 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


metallopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M64, N-terminal domain / Peptidase M64, IgA / Peptidase M64, N-terminal / Peptidase M64, N-terminal domain superfamily / IgA Peptidase M64 / Peptidase M64 N-terminus / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Immunoglobulin-like ...Peptidase M64, N-terminal domain / Peptidase M64, IgA / Peptidase M64, N-terminal / Peptidase M64, N-terminal domain superfamily / IgA Peptidase M64 / Peptidase M64 N-terminus / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Putative lipoprotein
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.17 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative peptidase (BF3526) from Bacteroides fragilis NCTC 9343 at 2.17 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative peptidase
B: putative peptidase
C: putative peptidase
D: putative peptidase
E: putative peptidase
F: putative peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,85281
Polymers278,5816
Non-polymers7,27175
Water35,0751947
1
A: putative peptidase
B: putative peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,95224
Polymers92,8602
Non-polymers2,09222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-167 kcal/mol
Surface area31410 Å2
MethodPISA
2
C: putative peptidase
D: putative peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,96535
Polymers92,8602
Non-polymers3,10533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-183 kcal/mol
Surface area30890 Å2
MethodPISA
3
E: putative peptidase
F: putative peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,93522
Polymers92,8602
Non-polymers2,07520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-157 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)238.730, 92.820, 173.890
Angle α, β, γ (deg.)90.000, 125.260, 90.000
Int Tables number5
Space group name H-MC121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY PROVIDES SUPPORTING EVIDENCE THAT A DIMER IS A SIGNIFICANT OLIGOMERIC STATE IN SOLUTION.

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
putative peptidase / Putative lipoprotein


Mass: 46430.191 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Strain: NCTC 9343 / Gene: BF3526, BF9343_3433 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5L9L3

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Non-polymers , 7 types, 2022 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1947 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT (RESIDUES 19-426) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 19-426) 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: 2.82 Å3/Da / Density % sol: 56.44 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20.00% Glycerol 20.00% polyethylene glycol 4000, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97941,0.97899
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2011
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
20.979411
30.978991
ReflectionResolution: 2.17→48.732 Å / Num. obs: 162812 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.817 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.17-2.250.7651.9629781656898.7
2.25-2.340.6182.4609511600398.9
2.34-2.440.5212.8581881525299.1
2.44-2.570.3933.6625961640999.2
2.57-2.730.34.7616721620999
2.73-2.940.2056.7618261621999.2
2.94-3.240.12510.3628671652599.3
3.24-3.70.07316.5607651606899
3.7-4.660.04523.7620831647299.1
4.660.0427.4622451675698.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.17→48.732 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.9448 / Occupancy max: 1 / Occupancy min: 0.23 / 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. PHOSPHATE, POLYETHENE GLYCOL, GLYCEROL, SODIUM AND CHLORIDE MODELED ARE PRESENT IN THE CRYSTALLIZATION/CRYO/PROTEIN BUFFER CONDITIONS. 3. THE MODELING OF THE ZINC (ZN) IONS IS SUPPORTED BY PEAKS IN THE ANOMALOUS DIFFERENCE FOURIER MAPS AND ZINC K EMISSION LINES IN X-RAY FLUORESCENCE EXCITATION SPECTRA. 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 6. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS)
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 8179 5.02 %RANDOM
Rwork0.1561 ---
obs0.1577 162808 99.24 %-
Displacement parametersBiso max: 140.75 Å2 / Biso mean: 37.341 Å2 / Biso min: 4.16 Å2
Baniso -1Baniso -2Baniso -3
1-4.1412 Å20 Å2-3.1263 Å2
2---0.3494 Å20 Å2
3----3.7918 Å2
Refine analyzeLuzzati coordinate error obs: 0.226 Å
Refinement stepCycle: LAST / Resolution: 2.17→48.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19214 0 400 1947 21561
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d9294SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes474HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2992HARMONIC5
X-RAY DIFFRACTIONt_it20367HARMONIC20
X-RAY DIFFRACTIONt_nbd10SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2662SEMIHARMONIC5
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_contact24082SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d20367HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg27650HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion2.69
LS refinement shellResolution: 2.17→2.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2249 597 5.01 %
Rwork0.2028 11308 -
all0.2039 11905 -
obs--99.24 %
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)
11.58130.182-0.31240.17330.11950.8253-0.03560.02550.1905-0.0394-0.02380.1084-0.171-0.04460.0594-0.10530.0033-0.0204-0.0524-0.0082-0.031672.689425.968841.067
20.8130.22150.02040.11820.07310.34420.05310.0072-0.0353-0.0068-0.0301-0.00090.0107-0.0621-0.023-0.0632-0.03480.00250.03020.0132-0.0491105.315214.011419.8036
30.40770.0787-0.22410.5293-0.02730.2805-0.0228-0.0463-0.05650.02730.0220.01030.0265-0.02160.0008-0.03010.00250.022-0.02890.0068-0.023110.748117.192782.7242
40.4452-0.1821-0.11060.5131-0.16380.2787-0.01520.00230.0191-0.01550.02710.0077-0.0290.0124-0.0119-0.0345-0.01890.0223-0.03630.0038-0.0139135.255711.183150.7463
51.00890.3368-0.30580.6774-0.18080.6395-0.0064-0.0262-0.2054-0.0855-0.0471-0.18140.15930.13730.0535-0.0696-0.02570.0361-0.0622-0.0136-0.032789.7608-24.27036.9535
60.9463-0.074-0.65840.57940.29581.04280.0880.0109-0.0524-0.0996-0.08450.1054-0.172-0.0582-0.0035-0.0424-0.0189-0.0122-0.0951-0.0054-0.040750.4526-21.123518.3341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|21 - 503 }A21 - 503
2X-RAY DIFFRACTION2{ B|21 - 503 }B21 - 503
3X-RAY DIFFRACTION3{ C|20 - 503 }C20 - 503
4X-RAY DIFFRACTION4{ D|19 - 503 }D19 - 503
5X-RAY DIFFRACTION5{ E|21 - 503 }E21 - 503
6X-RAY DIFFRACTION6{ F|20 - 503 }F20 - 503

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