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- PDB-3hdj: The crystal structure of probable ornithine cyclodeaminase from B... -

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Basic information

Entry
Database: PDB / ID: 3hdj
TitleThe crystal structure of probable ornithine cyclodeaminase from Bordetella pertussis Tohama I
ComponentsProbable ornithine cyclodeaminase
Keywordsstructural genomics / unknown function / APC62486 / ornithine cyclodeaminase / Bordetella pertussis Tohama I / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


ornithine cyclodeaminase, domain 1 / ornithine cyclodeaminase, domain 1 / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Probable ornithine cyclodeaminase
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsTan, K. / Sather, A. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of probable ornithine cyclodeaminase from Bordetella pertussis Tohama I
Authors: Tan, K. / Sather, A. / Clancy, S. / Joachimiak, A.
History
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 27, 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 / struct_conn / struct_site
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_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: Probable ornithine cyclodeaminase
B: Probable ornithine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,23314
Polymers65,5932
Non-polymers64012
Water9,008500
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-105 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.405, 50.923, 106.999
Angle α, β, γ (deg.)90.00, 100.98, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. The chains A and B are predicted to form a dimer.

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Components

#1: Protein Probable ornithine cyclodeaminase


Mass: 32796.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: Tohama I / Gene: Bordetella pertussis, BP0354 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q7VSP8
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.5M NaCl, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2008 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.7→39.5 Å / Num. all: 73662 / Num. obs: 73662 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 24.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.64 / Num. unique all: 3592 / % possible all: 97.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→39.41 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.82 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21189 3714 5 %RANDOM
Rwork0.1782 ---
all0.17993 69889 --
obs0.17993 69889 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.378 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.03 Å2
2--0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4556 0 34 500 5090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224848
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9746620
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.94421.98202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88315771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2091560
X-RAY DIFFRACTIONr_chiral_restr0.1090.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213733
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8671.53168
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50525047
X-RAY DIFFRACTIONr_scbond_it2.58331680
X-RAY DIFFRACTIONr_scangle_it4.1774.51547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 250 -
Rwork0.293 4978 -
obs-5228 97.07 %
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)
11.27220.0430.40150.30970.3121.77240.01060.0186-0.0510.0457-0.06850.07160.1119-0.3250.0580.1155-0.01710.01960.093-0.01510.0503-5.89813.03813.74
21.7326-0.16570.28350.4909-0.29841.22170.03440.0028-0.0943-0.0647-0.0709-0.05950.07690.1640.03640.10110.0090.02220.02640.0070.03726.51211.15438.113
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 310
2X-RAY DIFFRACTION2B0 - 310

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