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- PDB-4bxe: CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLE... -

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Basic information

Entry
Database: PDB / ID: 4bxe
TitleCRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH ANHYDROMURAMIC PENTAPEPTIDE
Components
  • AMPDH3
  • ANHYDROMURAMIC PEPTIDE
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX
Function / homology
Function and homology information


Gram-negative-bacterium-type cell wall / N-acetylmuramoyl-L-alanine amidase / peptidoglycan turnover / N-acetylmuramoyl-L-alanine amidase activity / outer membrane / peptidoglycan catabolic process / cell wall organization / metal ion binding
Similarity search - Function
Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / : / PGBD superfamily / Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily ...Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / : / PGBD superfamily / Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / PGBD-like superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsArtola-Recolons, C. / Hermoso, J.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Cell-Wall Remodeling by the Zinc-Protease Ampdh3 from Pseudomonas Aeruginosa.
Authors: Lee, M. / Artola-Recolons, C. / Carrasco-Lopez, C. / Martinez-Caballero, S. / Hesek, D. / Spink, E. / Lastochkin, E. / Zhang, W. / Hellman, L.M. / Boggess, B. / Hermoso, J.A. / Mobashery, S.
History
DepositionJul 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Atomic model / Structure summary
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AMPDH3
B: AMPDH3
C: ANHYDROMURAMIC PEPTIDE
D: ANHYDROMURAMIC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4819
Polymers59,0924
Non-polymers3895
Water1,31573
1
A: AMPDH3
B: AMPDH3
C: ANHYDROMURAMIC PEPTIDE
D: ANHYDROMURAMIC PEPTIDE
hetero molecules

A: AMPDH3
B: AMPDH3
C: ANHYDROMURAMIC PEPTIDE
D: ANHYDROMURAMIC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,96318
Polymers118,1848
Non-polymers77910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area21560 Å2
ΔGint-69 kcal/mol
Surface area49330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.940, 100.940, 165.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein AMPDH3


Mass: 28756.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9I5D1
#2: Protein/peptide ANHYDROMURAMIC PEPTIDE


Mass: 789.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 8

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.74 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.95→48.35 Å / Num. obs: 18710 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Biso Wilson estimate: 47.56 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 16.6
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameClassification
PHENIXmodel building
SCALAdata scaling
iMOSFLMphasing
SCALAphasing
MOLREPphasing
PHENIXphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AMPDH3-NATIVE

Resolution: 2.95→48.269 Å / SU ML: 0.53 / σ(F): 1.36 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 951 5.1 %
Rwork0.2032 --
obs0.2064 18648 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→48.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4182 0 26 73 4281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094317
X-RAY DIFFRACTIONf_angle_d1.4915869
X-RAY DIFFRACTIONf_dihedral_angle_d17.3251542
X-RAY DIFFRACTIONf_chiral_restr0.091620
X-RAY DIFFRACTIONf_plane_restr0.005773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.10550.41551300.34422473X-RAY DIFFRACTION100
3.1055-3.30.36731460.28462457X-RAY DIFFRACTION100
3.3-3.55480.31171370.24212477X-RAY DIFFRACTION100
3.5548-3.91240.23631370.18162492X-RAY DIFFRACTION100
3.9124-4.47810.22481550.15542503X-RAY DIFFRACTION100
4.4781-5.64060.21381280.16152566X-RAY DIFFRACTION100
5.6406-48.27540.23621180.18732729X-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)
11.50350.4564-0.87451.6215-0.47960.7489-0.01230.178-0.08440.18780.06520.12490.1072-0.3293-0.07720.3408-0.1426-0.03770.38390.04840.2533-1.89175.35129.1793
20.24040.6727-0.14631.3449-0.22791.9570.0207-0.42530.02170.54450.17120.42180.3492-0.3918-0.03440.6071-0.11710.0450.51350.15960.4629-4.93391.007122.209
32.1346-0.1676-0.40140.78260.63741.67440.1207-0.1830.15210.4003-0.01310.1439-0.0259-0.22-0.09570.5522-0.10470.10220.42590.07210.2957-6.121318.222530.2704
40.7725-0.3273-0.42111.28990.11160.90680.12750.08570.08160.15020.03230.0166-0.1321-0.0086-0.02020.2245-0.0743-0.06290.36010.04790.2256.03220.5547-3.5736
51.5398-0.55030.52651.5204-0.560.2451-0.1260.43620.8780.02280.27190.4512-1.13350.10030.01910.5913-0.00570.07840.50270.11110.68375.46441.1544-12.4317
61.4817-0.21550.15570.8981-0.60580.77930.09480.2353-0.0256-0.0085-0.0475-0.0356-0.1259-0.1689-0.01250.28210.0045-0.03030.42160.00690.2493-3.439324.9042-13.2893
71.7934-0.70980.01782.03010.57671.0479-0.0173-0.1180.06110.01360.010.0651-0.0976-0.22750.03540.307-0.0088-0.01960.47220.06740.2545-18.401335.4682-10.404
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 94 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 95 THROUGH 134 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 135 THROUGH 255 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 1 THROUGH 100 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 101 THROUGH 117 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 118 THROUGH 176 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 177 THROUGH 255 )

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