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- PDB-3cjp: Crystal structure of an uncharacterized amidohydrolase CAC3332 fr... -

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Basic information

Entry
Database: PDB / ID: 3cjp
TitleCrystal structure of an uncharacterized amidohydrolase CAC3332 from Clostridium acetobutylicum
ComponentsPredicted amidohydrolase, dihydroorotase family
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC / AMIDOHYDROLASE / CAC3332 / PSI-2
Function / homology
Function and homology information


secondary metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding / cytoplasm
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Predicted amidohodrolase (Dihydroorotase family)
Similarity search - Component
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsMalashkevich, V.N. / Toro, R. / Ramagopal, U.A. / Bonanno, J.B. / Meyer, A. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an uncharacterized amidohydrolase CAC3332 from Clostridium acetobutylicum.
Authors: Malashkevich, V.N. / Toro, R. / Ramagopal, U.A. / Bonanno, J.B. / Meyer, A. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _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
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted amidohydrolase, dihydroorotase family
B: Predicted amidohydrolase, dihydroorotase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8746
Polymers60,6122
Non-polymers2624
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-18.1 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.628, 77.273, 72.661
Angle α, β, γ (deg.)90.000, 96.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Predicted amidohydrolase, dihydroorotase family


Mass: 30306.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Species: Clostridium acetobutylicum / Strain: DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 / Gene: CA_C3337 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q97DY3
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Li sulfate, 0.1 M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2008
Details: Horizontal focusing sagital bend monocrystal and vertically focusing mirror
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 87364 / % possible obs: 99 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.061 / Χ2: 0.807 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.9220.31584460.446195.5
1.92-1.9920.22687430.494199.4
1.99-2.082.10.17288290.577199.8
2.08-2.192.10.12987650.63199.8
2.19-2.332.10.10787860.741199.8
2.33-2.512.10.08688440.76199.7
2.51-2.762.10.07287760.855199.8
2.76-3.162.10.06188011.103199.6
3.16-3.992.10.05188031.321199.7
3.99-502.10.03385711.106197.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.3.0034refinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→9.97 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.23 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2247 5.1 %RANDOM
Rwork0.184 ---
obs0.187 44323 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.383 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→9.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 4 343 4427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224166
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9745651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2045528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31625.904166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79415771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0951510
X-RAY DIFFRACTIONr_chiral_restr0.110.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023028
X-RAY DIFFRACTIONr_nbd_refined0.2190.22111
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22881
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2328
X-RAY DIFFRACTIONr_metal_ion_refined0.0380.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.218
X-RAY DIFFRACTIONr_mcbond_it1.4231.52709
X-RAY DIFFRACTIONr_mcangle_it4.439204278
X-RAY DIFFRACTIONr_scbond_it9.074201642
X-RAY DIFFRACTIONr_scangle_it4.9334.51370
LS refinement shellResolution: 1.85→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 152 -
Rwork0.234 2961 -
all-3113 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 33.7231 Å / Origin y: 45.7065 Å / Origin z: 53.2827 Å
111213212223313233
T-0.0791 Å2-0.0012 Å20.0098 Å2--0.0083 Å2-0.0022 Å2---0.0391 Å2
L0.314 °2-0.0045 °20.0261 °2-0.9561 °20.0927 °2--0.5064 °2
S-0.0159 Å °-0.0063 Å °-0.0131 Å °0.0062 Å °-0.0041 Å °0.064 Å °-0.0177 Å °-0.0605 Å °0.0199 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B3 - 264
2X-RAY DIFFRACTION1A3 - 264

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