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- PDB-3n6z: Crystal structure of a putative immunoglobulin A1 protease (BACOV... -

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Basic information

Entry
Database: PDB / ID: 3n6z
TitleCrystal structure of a putative immunoglobulin A1 protease (BACOVA_03286) from Bacteroides ovatus at 1.30 A resolution
Componentsputative immunoglobulin A1 protease
KeywordsHYDROLASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyPectate Lyase C-like - #110 / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative immunoglobulin A1 protease (BACOVA_03286) from Bacteroides ovatus at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 1.5Nov 27, 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: putative immunoglobulin A1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4266
Polymers37,9571
Non-polymers4685
Water7,999444
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: putative immunoglobulin A1 protease
hetero molecules

A: putative immunoglobulin A1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,85112
Polymers75,9142
Non-polymers93710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4140 Å2
ΔGint-56 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.679, 75.679, 132.101
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein putative immunoglobulin A1 protease


Mass: 37957.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_03286 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7LZL0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 20-381) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 20-381) 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 2.400000000M (NH4)2SO4, 0.1M Bicine pH 9.0, 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: 0.91162,0.97935,0.97899
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2010 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979351
30.978991
ReflectionResolution: 1.3→28.699 Å / Num. obs: 94721 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 11.259 Å2 / Rsym value: 0.084

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.3.15data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.3→28.699 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 1.309 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.039
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 THE ...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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL (GOL) AND SULFATE (SO4) MODELED ARE PRESENT IN CRYO/CRYSTALLIZATION CONDITIONS. 4. RAMACHANDRAN OUTLIER SER139 IS SUPPORTED BY DENSITY. THE N-TERMINAL REGION (29-35) HAS WEAK DENSITY. THE MODEL HERE IS LIKELY TO HAVE PARTIAL OCCUPANCY. 5. RESIDUES 20-28 AND 36-49 WERE NOT MODELED DUE TO THE LACK OF ELETRON DENSITY IN THESE REGIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.157 4739 5 %RANDOM
Rwork0.135 ---
obs0.137 94632 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.31 Å2 / Biso mean: 15.479 Å2 / Biso min: 6.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 28 444 2939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222781
X-RAY DIFFRACTIONr_bond_other_d0.0030.021838
X-RAY DIFFRACTIONr_angle_refined_deg1.521.953815
X-RAY DIFFRACTIONr_angle_other_deg1.12734545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7525412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95725.299117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.12915454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5731511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023297
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02565
X-RAY DIFFRACTIONr_mcbond_it2.12231792
X-RAY DIFFRACTIONr_mcbond_other1.3433776
X-RAY DIFFRACTIONr_mcangle_it2.92542886
X-RAY DIFFRACTIONr_scbond_it3.7795989
X-RAY DIFFRACTIONr_scangle_it5.2937892
X-RAY DIFFRACTIONr_rigid_bond_restr1.83534619
X-RAY DIFFRACTIONr_sphericity_free7.3953463
X-RAY DIFFRACTIONr_sphericity_bonded3.65934541
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 326 -
Rwork0.278 6564 -
all-6890 -
obs--99.68 %

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