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- PDB-6yra: Crystal structure of ATP-dependent caprolactamase from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 6yra
TitleCrystal structure of ATP-dependent caprolactamase from Pseudomonas jessenii
Components
  • 5-oxoprolinase
  • Hydantoinase
KeywordsHYDROLASE / Caprolactam hydrolase / nylon 6 monomer / 6-aminocaproic acid / 5-oxoproline / phosphocaprolactam / carboxyphosphate
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amides / 5-oxoprolinase (ATP-hydrolyzing) activity / glutathione metabolic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Hydantoinase B/oxoprolinase / Hydantoinase/oxoprolinase, N-terminal / Oxoprolinase family / : / Hydantoinase B/oxoprolinase / Hydantoinase/oxoprolinase N-terminal region / Hydantoinase/oxoprolinase C-terminal domain / Hydantoinase A/oxoprolinase / Hydantoinase/oxoprolinase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Caprolactamase subunit alpha / Caprolactamase subunit beta
Similarity search - Component
Biological speciesPseudomonas jessenii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4 Å
AuthorsRozeboom, H.J. / Janssen, D.B.
CitationJournal: Proteins / Year: 2021
Title: Catalytic and structural properties of ATP-dependent caprolactamase from Pseudomonas jessenii.
Authors: Marjanovic, A. / Rozeboom, H.J. / de Vries, M.S. / Mayer, C. / Otzen, M. / Wijma, H.J. / Janssen, D.B.
History
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Hydantoinase
A: 5-oxoprolinase
D: Hydantoinase
C: 5-oxoprolinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,5726
Polymers276,4414
Non-polymers1312
Water00
1
B: Hydantoinase
A: 5-oxoprolinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,2863
Polymers138,2202
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-66 kcal/mol
Surface area48820 Å2
MethodPISA
2
D: Hydantoinase
C: 5-oxoprolinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,2863
Polymers138,2202
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-24 kcal/mol
Surface area49910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.377, 167.367, 87.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN C
112(CHAIN B AND (RESID 2 THROUGH 281 OR RESID 283 THROUGH 580 OR RESID 600))
212(CHAIN D AND (RESID 2 THROUGH 281 OR RESID 283 THROUGH 580 OR RESID 600))

NCS ensembles :
ID
1
2

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Components

#1: Protein Hydantoinase


Mass: 62799.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas jessenii (bacteria) / Gene: CRX42_01180 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A2W0FH34
#2: Protein 5-oxoprolinase


Mass: 75420.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas jessenii (bacteria) / Gene: CRX42_01175 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A2W0EVE0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M Na/K phosphate, 0.1 M Bis-Tris propane, pH 7.5, and 20% PEG3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 2018
RadiationMonochromator: HeliosMX mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 4→48.84 Å / Num. obs: 24725 / % possible obs: 98.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.632 / Net I/σ(I): 2.3
Reflection shellResolution: 4→4.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.252 / Num. unique obs: 4389 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.18 Å48.84 Å
Translation7.18 Å48.84 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9W, 5M45, 5SVB

5l9w

5m45

5svb


Resolution: 4→48.84 Å / SU ML: 0.89 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 40.06
RfactorNum. reflection% reflection
Rfree0.381 1155 4.69 %
Rwork0.239 --
obs0.246 24622 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.88 Å2
Refinement stepCycle: LAST / Resolution: 4→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19263 0 2 0 19265
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A4234X-RAY DIFFRACTIONPOSITIONAL
12C4234X-RAY DIFFRACTIONPOSITIONAL
21B3500X-RAY DIFFRACTIONPOSITIONAL
22D3500X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.180.39281400.26342827X-RAY DIFFRACTION96
4.18-4.40.40821220.24612925X-RAY DIFFRACTION99
4.4-4.680.38751490.23992924X-RAY DIFFRACTION99
4.68-5.040.39171730.23922883X-RAY DIFFRACTION99
5.04-5.550.38611310.2672939X-RAY DIFFRACTION99
5.55-6.350.40881530.27122937X-RAY DIFFRACTION99
6.35-7.990.41281160.24722997X-RAY DIFFRACTION98
7.99-48.840.31961710.18183035X-RAY DIFFRACTION97
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)
10.26670.3830.44930.71380.0670.88890.00910.14030.1126-0.0869-0.11460.21450.091-0.02890.0840.1986-0.01040.07420.2573-0.01930.2699-55.1359.3584-23.4111
20.2358-0.31770.02341.7591-0.49810.26840.055-0.30060.01970.2879-0.02480.3966-0.0695-0.1725-0.02510.3926-0.00460.07180.44230.01060.3326-63.53793.612411.4579
30.8671-0.2036-0.01760.7957-0.4810.49360.01570.12050.1183-0.1833-0.0981-0.17090.01870.08460.09280.336-0.03970.03920.20470.00420.4207-18.014238.3696-36.4475
40.7997-0.05640.65010.2039-0.01951.3795-0.01410.05110.0978-0.067-0.0483-0.09860.1790.22050.06680.5051-0.00380.20560.39510.00130.62949.024225.7909-57.3327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'B' AND RESID 2 THROUGH 580)
2X-RAY DIFFRACTION2(CHAIN 'A' AND RESID 6 THROUGH 696)
3X-RAY DIFFRACTION3(CHAIN 'D' AND RESID 2 THROUGH 580)
4X-RAY DIFFRACTION4(CHAIN 'C' AND RESID 6 THROUGH 696)

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