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- PDB-2jah: Biochemical and structural analysis of the Clavulanic acid dehyde... -

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Basic information

Entry
Database: PDB / ID: 2jah
TitleBiochemical and structural analysis of the Clavulanic acid dehydeogenase (CAD) from Streptomyces clavuligerus
ComponentsCLAVULANIC ACID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / LACTAMASE INHIBITOR / ANTIBIOTIC BIOSYNTHESIS / NADPH / CLAVULANIC ACID
Function / homology
Function and homology information


short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Clavaldehyde dehydrogenase
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsMacKenzie, A.K. / Kershaw, N.J. / Hernandez, H. / Robinson, C.V. / Schofield, C.J. / Andersson, I.
CitationJournal: Biochemistry / Year: 2007
Title: Clavulanic Acid Dehydrogenase: Structural and Biochemical Analysis of the Final Step in the Biosynthesis of the Beta-Lactamase Inhibitor Clavulanic Acid
Authors: Mackenzie, A.K. / Kershaw, N.J. / Hernandez, H. / Robinson, C.V. / Schofield, C.J. / Andersson, I.
History
DepositionNov 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: CLAVULANIC ACID DEHYDROGENASE
B: CLAVULANIC ACID DEHYDROGENASE
C: CLAVULANIC ACID DEHYDROGENASE
D: CLAVULANIC ACID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7238
Polymers106,7414
Non-polymers2,9824
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.748, 122.626, 126.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 3 - 247 / Label seq-ID: 3 - 247

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
CLAVULANIC ACID DEHYDROGENASE


Mass: 26685.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Strain: NRRL3585 / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LCV7
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.2 Å3/Da / Density % sol: 42.7 %
Description: THE PDB ENTRY 1NFF WAS USED AS A MODEL TO ASSIST BUILDING.
Crystal growpH: 6.5
Details: 10% PEG 1000, 10% PEG 8000, 0.3 M SODIUM ACETATE, 0.05 M BIS-TRIS BUFFER (PH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 24, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND, GE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→29.92 Å / Num. obs: 82024 / % possible obs: 96.2 % / Observed criterion σ(I): 6 / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.7 / % possible all: 80.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCDphasing
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→29.92 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.765 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO ELECTRON DENSITY COULD BE OBSERVER FOR MET 1
RfactorNum. reflection% reflectionSelection details
Rfree0.209 4118 5 %RANDOM
Rwork0.182 ---
obs0.184 77845 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 192 494 8021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227663
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.98710447
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085985
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49323.333309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16151268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1781573
X-RAY DIFFRACTIONr_chiral_restr0.0780.21277
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025609
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.23826
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.25267
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2609
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4981.55008
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73627818
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.53432919
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4464.52629
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A972medium positional0.120.5
2B972medium positional0.110.5
3C972medium positional0.130.5
4D972medium positional0.120.5
1A841loose positional0.495
2B841loose positional0.525
3C841loose positional0.455
4D841loose positional0.585
1A972medium thermal0.682
2B972medium thermal0.542
3C972medium thermal0.482
4D972medium thermal0.462
1A841loose thermal1.3210
2B841loose thermal1.0710
3C841loose thermal0.9810
4D841loose thermal1.0810
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 231
Rwork0.221 4197
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)
11.3326-1.24020.14962.112-0.25570.94290.16330.1435-0.1105-0.3022-0.10220.2736-0.002-0.1153-0.0611-0.12210.0155-0.0344-0.1060.0181-0.106132.6418-5.964415.9009
21.6893-1.01170.32512.2795-0.14580.8105-0.5452-0.50320.09640.77180.56120.081-0.1853-0.1489-0.01590.11090.26220.02110.0508-0.0001-0.131435.277-2.955846.6357
31.3945-0.87840.21472.0279-0.04670.84080.17970.2521-0.064-0.3-0.1269-0.2050.13280.1811-0.0528-0.09480.05650.0098-0.0676-0.0093-0.093856.363-26.234916.5767
41.2623-1.17970.12262.3825-0.29630.8244-0.4467-0.3807-0.13420.71420.53350.02880.0943-0.0358-0.08680.08190.2204-0.0010.01620.024-0.113452.344-28.96647.1169
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 247
2X-RAY DIFFRACTION1A1248
3X-RAY DIFFRACTION2B3 - 247
4X-RAY DIFFRACTION2B1248
5X-RAY DIFFRACTION3C2 - 247
6X-RAY DIFFRACTION3C1248
7X-RAY DIFFRACTION4D3 - 247
8X-RAY DIFFRACTION4D1248

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