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

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Basic information

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


N-acetylmuramoyl-L-alanine amidase / Gram-negative-bacterium-type cell wall / 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 / PGBD-like 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
N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 / Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,8518
Polymers58,4374
Non-polymers1,4144
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-8.8 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.186, 101.186, 162.261
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 PEPTIDE /


Mass: 462.474 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SYNTHETIC CONSTRUCT (others)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside


Mass: 641.620 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAc[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_1*OC_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 10

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.38 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97166
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97166 Å / Relative weight: 1
ReflectionResolution: 3.1→48.3 Å / Num. obs: 15988 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Biso Wilson estimate: 46.43 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.8
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 7.6 / % 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: 3.1→48.3 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2772 759 5 %
Rwork0.2235 --
obs0.2262 15149 95.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 90 38 4264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0234335
X-RAY DIFFRACTIONf_angle_d1.8995904
X-RAY DIFFRACTIONf_dihedral_angle_d16.6621532
X-RAY DIFFRACTIONf_chiral_restr0.09636
X-RAY DIFFRACTIONf_plane_restr0.007769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.33930.36731340.35582689X-RAY DIFFRACTION91
3.3393-3.67530.37631610.27842724X-RAY DIFFRACTION93
3.6753-4.20680.28261410.21392876X-RAY DIFFRACTION96
4.2068-5.29910.20711640.17612949X-RAY DIFFRACTION98
5.2991-48.30550.2381590.1863152X-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)
12.0961-0.10060.29111.6035-1.54852.5689-0.0458-0.244-0.2226-0.06990.0718-0.1661-0.0404-0.1001-0.05680.19230.0602-0.01350.18380.01240.34158.7835-19.609845.6659
20.82020.50371.46690.70260.6662.8233-0.1923-0.15680.80690.0087-0.3268-0.0588-0.0854-0.4150.33730.13370.20920.11670.30610.09060.58666.9151-22.362341.667
32.30032.3913-0.18262.6523-0.18893.66740.1011-0.1691-0.37940.0307-0.0297-0.41390.4495-0.1545-0.11450.20980.0539-0.03050.34770.04940.39162.3713-29.233550.8458
42.83071.3795-0.60032.43660.04851.15850.1399-0.32520.07440.08710.11590.19880.0439-0.4956-0.20220.14510.02370.05840.40920.06080.3432-10.0263-28.230254.4927
57.13494.22162.28675.32761.51176.091-0.14740.42730.0127-0.27230.1373-0.08340.49650.0819-0.12290.20080.05190.0710.18810.03250.255-16.0857-36.697745.3577
68.1536-1.47590.13676.25734.93474.1133-0.0374-0.8538-0.25250.59110.04840.32840.0888-0.355-0.04870.24770.02130.06010.49110.13720.2305-16.0355-34.181154.5221
70.7082-0.35870.45911.485-0.7452.0611-0.03830.04250.2916-0.1158-0.1176-0.1029-0.2482-0.23160.13450.22760.02990.02780.27370.05970.4131-0.7762-4.214831.893
82.35591.19610.40163.19221.34153.0084-0.06620.26850.0441-0.5665-0.01020.4459-0.2217-0.6070.05440.30740.1107-0.07320.35820.06130.3028-5.2135-15.124513.8034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 66 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 67 THROUGH 84 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 85 THROUGH 132 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 133 THROUGH 189 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 190 THROUGH 229 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 230 THROUGH 255 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 1 THROUGH 84 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 85 THROUGH 255 )

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