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- PDB-3cne: Crystal structure of the putative protease I from Bacteroides the... -

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Basic information

Entry
Database: PDB / ID: 3cne
TitleCrystal structure of the putative protease I from Bacteroides thetaiotaomicron
ComponentsPutative protease I
KeywordsHYDROLASE / protease I / Structural genomics / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
: / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Protein ppBat
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsZhang, R. / Volkart, L. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the putative protease I from Bacteroides thetaiotaomicron.
Authors: Zhang, R. / Volkart, L. / Abdullah, J. / Joachimiak, A.
History
DepositionMar 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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.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_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 protease I
B: Putative protease I
C: Putative protease I
D: Putative protease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,51214
Polymers78,1774
Non-polymers1,33510
Water6,684371
1
A: Putative protease I
D: Putative protease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7567
Polymers39,0892
Non-polymers6675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-18.4 kcal/mol
Surface area14400 Å2
MethodPISA
2
B: Putative protease I
C: Putative protease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7567
Polymers39,0892
Non-polymers6675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-18.3 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.607, 68.021, 75.389
Angle α, β, γ (deg.)90.00, 109.81, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE.

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Components

#1: Protein
Putative protease I


Mass: 19544.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Species: Bacteroides thetaiotaomicron / Strain: VPI-5482 / DSM 2079 / NCTC 10582 / E50 / Gene: GI:29338570, BT_1263 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8A8A4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M CaCl2, 0.1M Tris-HCl pH 8.5, 25% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2006 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. all: 45542 / Num. obs: 45132 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 17.54
Reflection shellResolution: 1.99→2.045 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3.77 / Num. unique all: 3512 / % possible all: 91.46

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.99→36.35 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.898 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.193 / ESU R Free: 0.17
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23441 2417 5.1 %RANDOM
Rwork0.18593 ---
all0.18839 45132 --
obs0.18839 45132 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å2-0.19 Å2
2---0.33 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.99→36.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5331 0 58 371 5760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225489
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.9637421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7215691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.46826.552232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3615952
X-RAY DIFFRACTIONr_chiral_restr0.1030.2835
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024074
X-RAY DIFFRACTIONr_nbd_refined0.2250.22769
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2407
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.215
X-RAY DIFFRACTIONr_mcbond_it1.2161.53558
X-RAY DIFFRACTIONr_mcangle_it1.48525537
X-RAY DIFFRACTIONr_scbond_it2.73532270
X-RAY DIFFRACTIONr_scangle_it4.0744.51884
LS refinement shellResolution: 1.99→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 162 -
Rwork0.217 3050 -
obs-3212 91.46 %
Refinement TLS params.Method: refined / Origin x: 24.0404 Å / Origin y: 15.2406 Å / Origin z: 9.8183 Å
111213212223313233
T-0.0129 Å20.0131 Å20.0024 Å2--0.0249 Å2-0.0014 Å2---0.0246 Å2
L0.2813 °2-0.0215 °20.1207 °2-0.0837 °2-0.1413 °2--0.2879 °2
S-0.0159 Å °-0.0517 Å °-0.0289 Å °-0.0046 Å °0.0568 Å °-0.0019 Å °-0.034 Å °-0.0577 Å °-0.0409 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1752 - 175
2X-RAY DIFFRACTION1BB3 - 1753 - 175
3X-RAY DIFFRACTION1CC2 - 1752 - 175
4X-RAY DIFFRACTION1DD2 - 1752 - 175
5X-RAY DIFFRACTION1BM2011
6X-RAY DIFFRACTION1DN2011

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