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- PDB-1jwq: Structure of the catalytic domain of CwlV, N-acetylmuramoyl-L-ala... -

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Basic information

Entry
Database: PDB / ID: 1jwq
TitleStructure of the catalytic domain of CwlV, N-acetylmuramoyl-L-alanine amidase from Bacillus(Paenibacillus) polymyxa var.colistinus
ComponentsN-ACETYLMURAMOYL-L-ALANINE AMIDASE CwlV
KeywordsHYDROLASE / open alpha-beta-alpha
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Zn-dependent exopeptidases / AMIN domain / AMIN domain / Copper amine oxidase-like, N-terminal / Copper amine oxidase-like, N-terminal domain superfamily / : / Copper amine oxidase N-terminal domain / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase ...Zn-dependent exopeptidases / AMIN domain / AMIN domain / Copper amine oxidase-like, N-terminal / Copper amine oxidase-like, N-terminal domain superfamily / : / Copper amine oxidase N-terminal domain / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPaenibacillus polymyxa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsYamane, T. / Koyama, Y. / Nojiri, Y. / Hikage, T. / Akita, M. / Suzuki, A. / Shirai, T. / Ise, F. / Shida, T. / Sekiguchi, J.
CitationJournal: To be Published
Title: The Structure of the catalytic domain of N-acetylmuramoyl-L-alanine amidase, a cell wall hydrolase from Bacillus polymyxa var.colistinus and its resemblance to the structure of carboxypeptidases
Authors: Yamane, T. / Koyama, Y. / Nojiri, Y. / Hikage, T. / Akita, M. / Suzuki, A. / Shirai, T. / Ise, F. / Shida, T. / Sekiguchi, J.
History
DepositionSep 5, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-ACETYLMURAMOYL-L-ALANINE AMIDASE CwlV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7732
Polymers19,7071
Non-polymers651
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.500, 66.500, 88.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein N-ACETYLMURAMOYL-L-ALANINE AMIDASE CwlV


Mass: 19707.303 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus polymyxa (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LCR3, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.53 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 3, 1999 / Details: mirrors
RadiationMonochromator: the rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.708 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 185513 / Num. obs: 34876 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.092
Reflection shellResolution: 1.8→1.94 Å / Rmerge(I) obs: 0.198 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 871 4.97 %RANDOM
Rwork0.176 ---
all-18395 --
obs-17524 --
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å2-1.37 Å20 Å2
2---0.99 Å20 Å2
3---1.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1363 0 1 229 1593
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_deg0.65
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.24 153 -
Rwork0.212 --
obs-3081 94.5 %

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