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- PDB-1gq6: PROCLAVAMINATE AMIDINO HYDROLASE FROM STREPTOMYCES CLAVULIGERUS -

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Basic information

Entry
Database: PDB / ID: 1gq6
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 / SYNCHROTRON / MAD / Resolution: 1.75 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_asym_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_asym_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6529
Polymers100,3223
Non-polymers3306
Water10,305572
1
A: PROCLAVAMINATE AMIDINO HYDROLASE
B: PROCLAVAMINATE AMIDINO HYDROLASE
C: PROCLAVAMINATE AMIDINO HYDROLASE
hetero molecules

A: PROCLAVAMINATE AMIDINO HYDROLASE
B: PROCLAVAMINATE AMIDINO HYDROLASE
C: PROCLAVAMINATE AMIDINO HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,30418
Polymers200,6446
Non-polymers65912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)139.859, 78.931, 93.199
Angle α, β, γ (deg.)90.00, 123.90, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A9 - 68
2115B9 - 68
3115C9 - 68
1216A69 - 72
2216B69 - 72
3216C69 - 72
1315A73 - 151
2315B73 - 151
3315C73 - 151
1416A152 - 156
2416B152 - 156
3416C152 - 156
1515A157 - 351
2515B157 - 351
3515C157 - 351

NCS oper:
IDCodeMatrixVector
1given(-0.33389, 0.82358, 0.45851), (-0.82156, -0.49274, 0.28679), (0.46212, -0.28094, 0.84114)100.63581, 44.49427, -34.81046
2given(-0.33961, -0.81874, 0.46296), (0.81777, -0.5002, -0.28469), (0.46466, 0.28191, 0.83942)86.52071, -70.27638, -29.98474

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Components

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


Mass: 33440.738 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PET24A(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P37819, UniProt: P0DJQ3*PLUS, agmatinase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 1.9 Å3/Da / Density % sol: 36 %
Crystal growpH: 7.5
Details: 2.2 M AMMONIUM FORMATE, 200 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
32.2 Mammonium formate1reservoir
40.2 MHEPES1reservoirpH7.5
21drop3-fold molar excessMnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8855
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8855 Å / Relative weight: 1
ReflectionResolution: 1.75→54.76 Å / Num. obs: 82386 / % possible obs: 97.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 9.5
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.7 / % possible all: 89.7
Reflection
*PLUS
Num. measured all: 380778
Reflection shell
*PLUS
% possible obs: 89.7 % / Num. unique obs: 11034 / Num. measured obs: 27406

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Processing

Software
NameVersionClassification
REFMAC5.0.32refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.825 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17 4105 5 %RANDOM
Rwork0.142 ---
obs-78276 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6505 0 6 572 7083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216665
X-RAY DIFFRACTIONr_bond_other_d0.0010.026102
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.541.9569107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.801314080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1060.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027687
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021358
X-RAY DIFFRACTIONr_nbd_refined0.2280.31630
X-RAY DIFFRACTIONr_nbd_other0.1970.36148
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.5497
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3320.333
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3130.3163
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.527
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6861.54385
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19526992
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.98132280
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0254.52115
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.249 245
Rwork0.194 5095
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)
10.61380.18010.06090.8603-0.1370.96970.02780.0372-0.0218-0.08020.00270.08630.097-0.0977-0.03050.0383-0.014-0.01330.01950.00170.036454.8671-27.5541-12.7604
20.5501-0.19770.15970.90160.15160.92370.00530.04440.0678-0.0831-0.01850.053-0.1068-0.09310.01320.03280.0259-0.00320.0350.00910.036953.58389.1784-12.3821
30.9257-0.0272-0.02350.397-0.05381.15080.00450.0752-0.0222-0.0759-0.012-0.03460.03610.09870.00750.02050.00960.01840.03660.00110.018284.6109-7.7965-23.0158
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 309
2X-RAY DIFFRACTION2B9 - 309
3X-RAY DIFFRACTION3C9 - 309
Software
*PLUS
Name: REFMAC / Version: '5.0.32 18/01/2001' / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.142 / Rfactor Rfree: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.54

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