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- PDB-1gvg: Crystal Structure of Clavaminate Synthase with Nitric Oxide -

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Basic information

Entry
Database: PDB / ID: 1gvg
TitleCrystal Structure of Clavaminate Synthase with Nitric Oxide
ComponentsCLAVAMINATE SYNTHASE 1
KeywordsOXIDOREDUCTASE / LYASE / OXYGENASE / TRIFUNCTIONAL ENZYME / CLAVAMINATE SYNTHASE 1 / JELLY ROLL / NITRIC OXIDE
Function / homology
Function and homology information


clavaminate synthase / clavaminate synthase activity / clavulanic acid biosynthetic process / antibiotic biosynthetic process / iron ion binding
Similarity search - Function
Clavaminate synthase-like / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / HYDROXYAMINE / DEOXYGUANIDINOPROCLAVAMINIC ACID / Clavaminate synthase 1
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsZhang, Z.H. / Ren, J. / McKinnon, C.H. / Clifton, I.J. / Harlos, K. / Schofield, C.J.
Citation
Journal: FEBS Lett. / Year: 2002
Title: Crystal Structure of a Clavaminate Synthase-Fe(II) -2-Oxoglutarate-Substrate-No Complex: Evidence for Metal Centered Rearrangements
Authors: Zhang, Z.H. / Ren, J. / Harlos, K. / McKinnon, C.H. / Clifton, I.J. / Schofield, C.J.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: Structural Origins of the Selectivity of the Trifunctional Oxygenase Clavaminic Acid Synthase
Authors: Zhang, Z.H. / Ren, J. / Stammers, D.K. / Baldwin, J.E. / Harlos, K. / Schofield, C.J.
History
DepositionFeb 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software
Revision 1.4May 23, 2018Group: Data collection / Database references / Structure summary
Category: citation_author / struct / Item: _citation_author.name / _struct.title
Revision 1.5Dec 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLAVAMINATE SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1678
Polymers35,4161
Non-polymers7517
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.270, 69.520, 70.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CLAVAMINATE SYNTHASE 1 / / CLAVAMINIC ACID SYNTHASE 1 / CAS1


Mass: 35415.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q05581, clavaminate synthase

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Non-polymers , 6 types, 399 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PCX / DEOXYGUANIDINOPROCLAVAMINIC ACID


Mass: 228.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N4O3
#6: Chemical ChemComp-HOA / HYDROXYAMINE / Hydroxylamine


Mass: 33.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3NO
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.2 Å3/Da / Density % sol: 43.65 %
Crystal growpH: 7.6 / Details: pH 7.60
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
2100 mMTris1reservoirpH7.5
32.0 Mammonium sulfate1reservoir
410 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→30 Å / Num. obs: 46381 / % possible obs: 97.7 % / Redundancy: 13.2 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 29.1
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 4.46 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.8 / % possible all: 86
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 301822
Reflection shell
*PLUS
% possible obs: 86 % / Num. unique obs: 4038

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DS0

1ds0


Resolution: 1.54→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 2325 4.9 %RANDOM
Rwork0.1842 ---
obs0.1842 46333 98.2 %-
Solvent computationBsol: 46.29 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.968 Å20 Å20 Å2
2---0.586 Å20 Å2
3---1.554 Å2
Refinement stepCycle: LAST / Resolution: 1.54→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 44 392 2870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PCX-NO.PARPCX-NO.TOP
X-RAY DIFFRACTION2AKG.PARAKG.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2074 / Rfactor Rwork: 0.1813
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6

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