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- PDB-9g5m: N-Acyl-D-amino-acid deacylase (D-acylase) from Klebsiella pneumon... -

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Basic information

Entry
Database: PDB / ID: 9g5m
TitleN-Acyl-D-amino-acid deacylase (D-acylase) from Klebsiella pneumoniae in an open conformation
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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Amidohydrolase family protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae Kp13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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
DepositionJul 17, 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)55,66624
Polymers53,5691
Non-polymers2,09723
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-70 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.774, 100.774, 125.721
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#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
Plasmid: pET22b+ / 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

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Non-polymers , 7 types, 397 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.44 Å3/Da / Density % sol: 64.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.27→125.72 Å / Num. obs: 34890 / % possible obs: 99.9 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.214 / Net I/σ(I): 7.7
Reflection shellResolution: 2.27→2.33 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.246 / Num. unique obs: 820

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Processing

Software
NameVersionClassification
PHENIX1.21.1-5286refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→71.69 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1729 5 %randown
Rwork0.157 ---
obs-34842 99.9 %-
Displacement parametersBiso mean: 34 Å2
Refinement stepCycle: LAST / Resolution: 2.27→71.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 124 378 4201
LS refinement shellResolution: 2.27→2.33 Å
RfactorNum. reflection
Rfree0.2576 154
Rwork0.2281 -
obs-2881
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)
11.43020.33160.04731.9865-0.6592.2426-0.01890.05460.0067-0.0316-0.0275-0.1424-0.03460.20540.04370.1576-0.0065-0.00630.2569-0.01250.1584-28.848338.188111.589
24.920.23891.03192.47511.44921.12430.182-0.2258-0.25730.1713-0.116-0.25870.17840.0283-0.05010.184-0.04-0.01550.29140.02940.1301-21.192736.331627.0062
32.33130.1869-0.3081.3437-0.74150.73260.06150.2763-0.1938-0.2271-0.02960.10460.22990.0004-0.04410.26370.0019-0.00940.2572-0.01450.1573-43.224129.05655.8206
41.5230.2991-0.29430.8586-0.02120.92650.01310.20020.1166-0.1106-0.00690.0349-0.1369-0.1558-0.01060.25630.0322-0.00050.30320.02570.1962-52.55746.96513.5028
50.2995-0.0444-0.41370.18591.12566.4662-0.01310.0944-0.0075-0.08220.0267-0.01410.1159-0.1162-0.02060.2169-0.0631-0.00950.2990.0090.2109-35.087142.2951-14.7307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 372 through 479 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 143 )
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 283 )
5X-RAY DIFFRACTION5chain 'A' and (resid 284 through 371 )

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