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- PDB-4rn7: The crystal structure of N-acetylmuramoyl-L-alanine amidase from ... -

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Basic information

Entry
Database: PDB / ID: 4rn7
TitleThe crystal structure of N-acetylmuramoyl-L-alanine amidase from Clostridium difficile 630
ComponentsN-acetylmuramoyl-L-alanine amidase
KeywordsHYDROLASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / outer membrane-bounded periplasmic space / membrane / metal ion binding
Similarity search - Function
Zn-dependent exopeptidases / : / 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
FORMIC ACID / N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.717 Å
AuthorsTan, K. / Mulligan, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile.
Authors: Rosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. / Kim, Y. / Maltseva, N. / Osipiuk, J. / ...Authors: Rosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. / Kim, Y. / Maltseva, N. / Osipiuk, J. / Minor, W. / Joachimiak, A. / Savchenko, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionOct 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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 1.3Mar 25, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6127
Polymers20,8861
Non-polymers7266
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.407, 66.407, 96.200
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 N-acetylmuramoyl-L-alanine amidase


Mass: 20886.156 Da / Num. of mol.: 1 / Fragment: UNP residues 117-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Strain: 630 / Gene: CD630_27610 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: Q183J9, N-acetylmuramoyl-L-alanine amidase

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Non-polymers , 5 types, 129 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 25% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2013 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 1.72→28.8 Å / Num. all: 26769 / Num. obs: 26769 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 8.3 % / Biso Wilson estimate: 27.45 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 54.7
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1344 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDBuilder/HKL3000phasing
MLPHAREBuilder/HKL3000phasing
DMBuilder/HKL3000model building
DENZOBuilder/HKL3000data reduction
SCALEPACKBuilder/HKL3000data scaling
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMBuilder/HKL3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.717→28.755 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 1322 4.95 %random
Rwork0.1948 ---
obs0.1959 26718 99.73 %-
all-26718 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.717→28.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1426 0 29 123 1578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061520
X-RAY DIFFRACTIONf_angle_d0.9882067
X-RAY DIFFRACTIONf_dihedral_angle_d13.634578
X-RAY DIFFRACTIONf_chiral_restr0.068240
X-RAY DIFFRACTIONf_plane_restr0.003270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7171-1.78580.28451580.2472768X-RAY DIFFRACTION100
1.7858-1.86710.28981250.2342793X-RAY DIFFRACTION100
1.8671-1.96550.2851760.22282770X-RAY DIFFRACTION100
1.9655-2.08860.25421380.20962807X-RAY DIFFRACTION100
2.0886-2.24980.1871190.19532830X-RAY DIFFRACTION100
2.2498-2.47610.22811630.19892787X-RAY DIFFRACTION100
2.4761-2.83420.2151330.20912851X-RAY DIFFRACTION100
2.8342-3.56970.23011460.19282864X-RAY DIFFRACTION100
3.5697-28.75910.1871640.17922926X-RAY DIFFRACTION98
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)
18.85073.3388-3.77467.2895-3.99952.70520.31880.8530.3433-0.46180.32440.05630.6311-0.6947-0.64240.3072-0.0617-0.00650.23580.03440.2491-27.35315.6623-17.1819
23.875-0.41330.77255.69581.20620.45120.0807-0.4889-0.16330.821-0.0114-0.38120.09240.23360.02070.3681-0.127-0.02650.22710.02790.3267-26.12936.5523-0.0284
32.75931.305-0.20385.3802-1.5372.9316-0.03040.1630.0888-0.05310.0850.3515-0.0283-0.2306-0.04140.2482-0.07730.01340.2148-0.00930.2339-35.7099.7308-6.9408
42.8937-2.87472.95073.221-3.77337.613-0.03340.3861-0.166-1.0166-0.0761-0.22240.4262-0.14220.05950.5391-0.12910.05190.3762-0.02150.4008-30.61062.582-15.6479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 114 through 123 )
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 276 )
4X-RAY DIFFRACTION4chain 'A' and (resid 277 through 299 )

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