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- PDB-3rha: The crystal structure of Oxidoreductase from Arthrobacter aurescens -

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Basic information

Entry
Database: PDB / ID: 3rha
TitleThe crystal structure of Oxidoreductase from Arthrobacter aurescens
ComponentsPutrescine oxidase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / ABM06930.1.
Function / homology
Function and homology information


putrescine oxidase / putrescine oxidase activity
Similarity search - Function
Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Putrescine oxidase
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.052 Å
AuthorsZhang, Z. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: The crystal structure of Oxidoreductase from Arthrobacter aurescens
Authors: Zhang, Z. / Almo, S.C. / Swaminathan, S.
History
DepositionApr 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putrescine oxidase
B: Putrescine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7015
Polymers106,0342
Non-polymers1,6673
Water17,655980
1
A: Putrescine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8052
Polymers53,0171
Non-polymers7881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putrescine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8973
Polymers53,0171
Non-polymers8802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.644, 117.905, 165.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putrescine oxidase /


Mass: 53017.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Strain: TC1 / Gene: puo, AAur_0043 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)ripl / References: UniProt: A1R0W1, putrescine oxidase
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 980 / 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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8 M ammonium citrate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 77476 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 2.3
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.3 / Num. unique all: 7456 / % possible all: 97.5

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2C27

2c27


Resolution: 2.052→49.986 Å / SU ML: 0.24 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.09 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 3762 5.04 %RANDOM
Rwork0.1575 ---
obs0.1594 74657 96.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.771 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.6252 Å20 Å2-0 Å2
2--2.8095 Å20 Å2
3----6.4347 Å2
Refinement stepCycle: LAST / Resolution: 2.052→49.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7000 0 112 980 8092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057283
X-RAY DIFFRACTIONf_angle_d0.9329910
X-RAY DIFFRACTIONf_dihedral_angle_d17.9822662
X-RAY DIFFRACTIONf_chiral_restr0.0611071
X-RAY DIFFRACTIONf_plane_restr0.0051287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0523-2.07830.23761160.18332329X-RAY DIFFRACTION86
2.0783-2.10560.22561360.16622419X-RAY DIFFRACTION91
2.1056-2.13450.19381270.16632488X-RAY DIFFRACTION92
2.1345-2.1650.23081360.16062471X-RAY DIFFRACTION91
2.165-2.19730.21131250.16252471X-RAY DIFFRACTION93
2.1973-2.23160.22571480.15722548X-RAY DIFFRACTION94
2.2316-2.26820.19351440.15352509X-RAY DIFFRACTION94
2.2682-2.30730.18531340.15892579X-RAY DIFFRACTION95
2.3073-2.34930.22951200.15312533X-RAY DIFFRACTION95
2.3493-2.39450.20351410.14972609X-RAY DIFFRACTION95
2.3945-2.44330.20081520.16142572X-RAY DIFFRACTION96
2.4433-2.49650.20231210.15862626X-RAY DIFFRACTION96
2.4965-2.55450.19851300.16112603X-RAY DIFFRACTION97
2.5545-2.61840.231340.1662654X-RAY DIFFRACTION97
2.6184-2.68920.19731260.16852667X-RAY DIFFRACTION98
2.6892-2.76830.23621480.17322623X-RAY DIFFRACTION97
2.7683-2.85770.22151490.17512662X-RAY DIFFRACTION98
2.8577-2.95980.22771540.17442670X-RAY DIFFRACTION98
2.9598-3.07830.22261490.16952663X-RAY DIFFRACTION98
3.0783-3.21840.21621520.16662689X-RAY DIFFRACTION99
3.2184-3.3880.20341460.1532727X-RAY DIFFRACTION99
3.388-3.60020.15911470.14482728X-RAY DIFFRACTION99
3.6002-3.87810.16431510.13982732X-RAY DIFFRACTION100
3.8781-4.26820.13761360.13042769X-RAY DIFFRACTION100
4.2682-4.88530.14071350.12272797X-RAY DIFFRACTION100
4.8853-6.15320.16481440.15282822X-RAY DIFFRACTION100
6.1532-50.00030.19151610.16552935X-RAY DIFFRACTION100

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