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- PDB-1gq7: PROCLAVAMINATE AMIDINO HYDROLASE FROM STREPTOMYCES CLAVULIGERUS -

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Basic information

Entry
Database: PDB / ID: 1gq7
TitlePROCLAVAMINATE AMIDINO HYDROLASE FROM STREPTOMYCES CLAVULIGERUS
ComponentsPROCLAVAMINATE AMIDINO HYDROLASE
KeywordsHYDROLASE / CLAVAMINATE / CLAVAMINIC / PAH / ARGINASE / ANTIBIOTIC
Function / homology
Function and homology information


proclavaminate amidinohydrolase / proclavaminate amidinohydrolase activity / clavulanic acid biosynthetic process / putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / metal ion binding
Similarity search - Function
Agmatinase-related / Ureohydrolase domain / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Proclavaminate amidinohydrolase / Proclavaminate amidinohydrolase
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsElkins, J.M. / Clifton, I.J. / Hernandez, H. / Robinson, C.V. / Schofield, C.J. / Hewitson, K.S.
CitationJournal: Biochem. J. / Year: 2002
Title: Oligomeric structure of proclavaminic acid amidino hydrolase: evolution of a hydrolytic enzyme in clavulanic acid biosynthesis.
Authors: Elkins, J.M. / Clifton, I.J. / Hernandez, H. / Doan, L.X. / Robinson, C.V. / Schofield, C.J. / Hewitson, K.S.
History
DepositionNov 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROCLAVAMINATE AMIDINO HYDROLASE
B: PROCLAVAMINATE AMIDINO HYDROLASE
C: PROCLAVAMINATE AMIDINO HYDROLASE
D: PROCLAVAMINATE AMIDINO HYDROLASE
E: PROCLAVAMINATE AMIDINO HYDROLASE
F: PROCLAVAMINATE AMIDINO HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,30418
Polymers200,6446
Non-polymers65912
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.922, 81.348, 120.389
Angle α, β, γ (deg.)90.00, 99.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.06587, 0.71882, -0.69207), (-0.6453, -0.49833, -0.57901), (-0.76109, 0.48473, 0.43103)31.68792, -80.28507, 20.63102
2given(0.0693, -0.64711, -0.75924), (0.71251, -0.50058, 0.49169), (-0.69823, -0.57504, 0.42638)-38.26785, -73.17609, -33.1874
3given(-0.99772, -0.06749, -0.00152), (-0.06747, 0.99631, 0.05305), (-0.00206, 0.05304, -0.99859)-61.11634, -3.651, 62.51112
4given(-0.02438, -0.68328, 0.72975), (-0.68629, -0.51934, -0.5092), (0.72691, -0.51324, -0.45627)-87.38945, -84.66604, 37.43931
5given(-0.11032, 0.68006, 0.72481), (0.67029, -0.48756, 0.55947), (0.73386, 0.54755, -0.40205)-17.94106, -75.6867, 91.85432

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Components

#1: Protein
PROCLAVAMINATE AMIDINO HYDROLASE / PROCLAVAMINATE AMIDINO HYDROLASE UREOHYDROLASE


Mass: 33440.738 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PET24A(+) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: P37819, UniProt: P0DJQ3*PLUS, agmatinase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.28 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5 / Details: 24% PEG 400, 100 MM HEPES PH7.5, pH 7.50
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
111 mg/mlprotein1drop
324 %(v/v)PEG4001reservoir
40.1 MHEPES1reservoirpH7.5
50.2 M1reservoirCaCl2
21drop3-fold molar excessMnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2001 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→35.58 Å / Num. obs: 65708 / % possible obs: 98.5 % / Redundancy: 4 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.1
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.3 / % possible all: 92.6
Reflection
*PLUS
Num. measured all: 262831
Reflection shell
*PLUS
% possible obs: 98.5 % / Num. unique obs: 8947 / Num. measured obs: 31969

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GQ6

1gq6


Resolution: 2.45→35.59 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2244495 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES WHOSE SIDE-CHAINS WERE NOT VISIBLE WERE MODELLED AS ALANINE
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3296 5 %RANDOM
Rwork0.222 ---
obs0.222 65691 98.5 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.340988 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--9.02 Å20 Å2-6.3 Å2
2--0.43 Å20 Å2
3---8.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.45→35.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13113 0 12 332 13457
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.041.5
X-RAY DIFFRACTIONc_mcangle_it1.72
X-RAY DIFFRACTIONc_scbond_it1.522
X-RAY DIFFRACTIONc_scangle_it2.212.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 513 5 %
Rwork0.273 9706 -
obs--92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97
LS refinement shell
*PLUS
Rfactor obs: 0.173

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