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- PDB-2jap: Clavulanic Acid Dehydrogenase: Structural and Biochemical Analysi... -

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Basic information

Entry
Database: PDB / ID: 2jap
TitleClavulanic Acid Dehydrogenase: Structural and Biochemical Analysis of the Final Step in the Biosynthesis of the beta-Lactamase Inhibitor Clavulanic acid
ComponentsCLAVALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / ANTIBIOTIC BIOSYNTHESIS / BETA-LACTAMASE INHIBITOR
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
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-J01 / Chem-NDP / Clavaldehyde dehydrogenase
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 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 29, 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 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLAVALDEHYDE DEHYDROGENASE
B: CLAVALDEHYDE DEHYDROGENASE
C: CLAVALDEHYDE DEHYDROGENASE
D: CLAVALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,20712
Polymers105,4284
Non-polymers3,7788
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19440 Å2
ΔGint-60.6 kcal/mol
Surface area30960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.076, 123.423, 126.780
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: 3 / 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
CLAVALDEHYDE DEHYDROGENASE / CLAVULANIC ACID DEHYDROGENASE


Mass: 26357.094 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: Chemical
ChemComp-J01 / (2R,3Z,5R)-3-(2-HYDROXYETHYLIDENE)-7-OXO-4-OXA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / CLAVULANIC ACID


Mass: 199.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H9NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 42.5 %
Description: SELENOMETHIONINE STRUCTURE USED FOR RIGID BODY REFINEMENT WITH ISOMORPHOUS CRYSTALS
Crystal growpH: 6.5
Details: 25% PEG 2000,MONOMETHYL ETHER, 0.8 M SODIUM FORMATE, 0.1 M CACODYLATE BUFFER (PH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→34.9 Å / Num. obs: 53663 / % possible obs: 99.4 % / Observed criterion σ(I): 6 / Redundancy: 4.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 2.1→2.1 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.4 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.1→34.86 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 10.618 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2713 5.1 %RANDOM
Rwork0.184 ---
obs0.186 50900 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 248 253 7836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217696
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.99610496
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7775979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60223.333309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.753151259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2191573
X-RAY DIFFRACTIONr_chiral_restr0.0780.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025637
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.23771
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.25261
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2460
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3381.55020
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.51527785
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.24332971
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0084.52703
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
1A976tight positional0.030.05
2B976tight positional0.030.05
3C976tight positional0.030.05
4D976tight positional0.030.05
1A845loose positional0.515
2B845loose positional0.485
3C845loose positional0.475
4D845loose positional0.575
1A976tight thermal0.070.5
2B976tight thermal0.060.5
3C976tight thermal0.060.5
4D976tight thermal0.060.5
1A845loose thermal0.910
2B845loose thermal0.810
3C845loose thermal0.8110
4D845loose thermal0.8410
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 200
Rwork0.232 3657
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)
12.3367-1.59250.32263.0011-0.4741.44880.130.30350.0808-0.4706-0.07350.4009-0.0369-0.1577-0.0565-0.1438-0.0069-0.061-0.12820.0594-0.1432.191-6.043215.9399
22.3678-1.19850.62773.0610.05831.5559-0.5731-0.69520.32650.9140.58720.0853-0.2927-0.2025-0.01410.13030.2708-0.00140.0342-0.0548-0.142234.9191-2.993546.739
32.5633-1.24190.25762.9455-0.09631.37270.20310.4461-0.0505-0.4667-0.1316-0.38130.13790.2788-0.0715-0.14240.04110.0349-0.09-0.0251-0.14855.7317-26.177616.5769
42.0985-1.53910.21073.2933-0.36051.5549-0.4642-0.567-0.22940.86510.5977-0.08710.1371-0.0622-0.13360.06410.2077-0.0418-0.02290.016-0.161151.7572-28.947747.171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 247
2X-RAY DIFFRACTION1A1248
3X-RAY DIFFRACTION1A1249
4X-RAY DIFFRACTION2B3 - 247
5X-RAY DIFFRACTION2B1248
6X-RAY DIFFRACTION2B1249
7X-RAY DIFFRACTION3C2 - 247
8X-RAY DIFFRACTION3C1248
9X-RAY DIFFRACTION3C1249
10X-RAY DIFFRACTION4D3 - 247
11X-RAY DIFFRACTION4D1248
12X-RAY DIFFRACTION4D1249

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