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- PDB-9gv8: N-Acyl-D-amino-acid deacylase (D-acylase) from Klebsiella pneumon... -

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Basic information

Entry
Database: PDB / ID: 9gv8
TitleN-Acyl-D-amino-acid deacylase (D-acylase) from Klebsiella pneumoniae in the absence of glycerol
ComponentsAmidohydrolase family protein
KeywordsHYDROLASE / N-ACYL-D-AMINO-ACID DEACYLASE / D-ACYLASE / AMIDOHYDROLASE
Function / homology
Function and homology information


N-acyl-D-amino-acid deacylase / N-acyl-D-amino-acid deacylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
Similarity search - Function
D-aminoacylase, insert domain superfamily / Amidohydrolase 3 / Amidohydrolase family / : / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolase
Similarity search - Domain/homology
NICKEL (II) ION / Amidohydrolase family protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae Kp13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGavira, J.A. / Martinez-Rodriguez, S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-116261GB-I00 Spain
CitationJournal: Microb Biotechnol / Year: 2025
Title: Revisiting D-Acylases for D-Amino Acid Production.
Authors: Martinez-Rodriguez, S. / Gavira, J.A.
History
DepositionSep 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amidohydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,31911
Polymers53,5691
Non-polymers75010
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-71 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.422, 101.422, 124.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Amidohydrolase family protein / D-aminoacylase


Mass: 53568.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae Kp13 (bacteria)
Gene: dan, B5L96_17380, B6I68_16395, BANRA_04485, BL124_00028775, DW281_07100, EAO17_17410, FXN67_23300, G4V31_23420, GJJ08_023370, GJJ13_021835, GJJ18_03715, GNF00_21165, NCTC11679_04932, NCTC13443_ ...Gene: dan, B5L96_17380, B6I68_16395, BANRA_04485, BL124_00028775, DW281_07100, EAO17_17410, FXN67_23300, G4V31_23420, GJJ08_023370, GJJ13_021835, GJJ18_03715, GNF00_21165, NCTC11679_04932, NCTC13443_01470, NCTC5052_02702, NCTC9601_05682, NCTC9661_05441, QIG75_04865, SAMEA3499874_02915, SAMEA3499901_00964, SAMEA3512100_03687, SAMEA3515122_03158, SAMEA3538658_01149, SAMEA3538828_01003, SAMEA3673026_03520, SAMEA3720909_04521, SAMEA4364603_03367, SAMEA4873597_03320, SAMEA4873632_03948, VKR_04363
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: W9BIW9, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, N-acyl-D-amino-acid deacylase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop
Details: HRI: 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50.91 Å / Num. obs: 23169 / % possible obs: 99.3 % / Redundancy: 5.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.079 / Rrim(I) all: 0.185 / Χ2: 0.88 / Net I/σ(I): 5.4 / Num. measured all: 120947
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 4.3 % / Rmerge(I) obs: 2.739 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2677 / CC1/2: 0.46 / Rpim(I) all: 1.446 / Rrim(I) all: 3.117 / Χ2: 0.88

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50.91 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 1119 4.87 %
Rwork0.2262 --
obs0.2282 22989 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→50.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3691 0 38 67 3796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023993
X-RAY DIFFRACTIONf_angle_d0.4975441
X-RAY DIFFRACTIONf_dihedral_angle_d13.7261522
X-RAY DIFFRACTIONf_chiral_restr0.043591
X-RAY DIFFRACTIONf_plane_restr0.004727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.42791270.41072472X-RAY DIFFRACTION91
2.72-2.860.33651270.34782696X-RAY DIFFRACTION99
2.86-3.040.36351440.31442742X-RAY DIFFRACTION100
3.04-3.280.34891440.29872755X-RAY DIFFRACTION100
3.28-3.60.29681690.24962700X-RAY DIFFRACTION100
3.61-4.130.25611570.2172743X-RAY DIFFRACTION99
4.13-5.20.2358940.1752856X-RAY DIFFRACTION100
5.2-50.910.20771570.18442906X-RAY DIFFRACTION100
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)
14.06351.77221.6371.63510.80731.57720.1968-0.0058-0.26530.0371-0.0892-0.22920.11050.1973-0.12190.3575-0.0486-0.00570.63920.07160.5081-25.686934.911220.3656
22.6024-1.2555-0.75751.9785-0.57571.66090.13210.4811-0.3133-0.1717-0.15740.26050.4708-0.23080.04220.4701-0.0307-0.03630.662-0.030.5887-45.944428.64875.0414
31.64120.6063-1.22840.5744-0.13732.1475-0.06490.72370.2305-0.20040.13540.1448-0.2642-0.4697-0.04880.46190.0134-0.06370.79980.14550.5436-45.574745.3874-3.7892
41.70920.47990.75522.7117-0.38253.19420.09920.34620.0107-0.2527-0.0186-0.12270.0460.4324-0.10920.3633-0.0124-0.02510.50670.04770.4623-28.700838.22911.4549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 371 )
4X-RAY DIFFRACTION4chain 'A' and (resid 372 through 478 )

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