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- PDB-4bol: Crystal structure of AmpDh2 from Pseudomonas aeruginosa in comple... -

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Basic information

Entry
Database: PDB / ID: 4bol
TitleCrystal structure of AmpDh2 from Pseudomonas aeruginosa in complex with pentapeptide
ComponentsAMPDH2
KeywordsHYDROLASE
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 / 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 / Peptidoglycan binding-like ...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 / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-J0J / N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsArtola-Recolons, C. / Martinez-Caballero, S. / Lee, M. / Carrasco-Lopez, C. / Hesek, D. / Spink, E.E. / Lastochkin, E. / Zhang, W. / Hellman, L.M. / Boggess, B. ...Artola-Recolons, C. / Martinez-Caballero, S. / Lee, M. / Carrasco-Lopez, C. / Hesek, D. / Spink, E.E. / Lastochkin, E. / Zhang, W. / Hellman, L.M. / Boggess, B. / Mobashery, S. / Hermoso, J.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Reaction Products and the X-Ray Structure of Ampdh2, a Virulence Determinant of Pseudomonas Aeruginosa.
Authors: Martinez-Caballero, S. / Lee, M. / Artola-Recolons, C. / Carrasco-Lopez, C. / Hesek, D. / Spink, E.E. / Lastochkin, E. / Zhang, W. / Hellman, L.M. / Boggess, B. / Mobashery, S. / Hermoso, J.A.
History
DepositionMay 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Atomic model / Other
Revision 1.2Jul 31, 2013Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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 / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMPDH2
B: AMPDH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9416
Polymers57,8882
Non-polymers1,0544
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-89.6 kcal/mol
Surface area21830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.630, 97.234, 104.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AMPDH2


Mass: 28943.820 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HT86
#2: Chemical ChemComp-J0J / D-alanyl-N-[(2S,6R)-6-amino-6-carboxy-1-{[(1R)-1-carboxyethyl]amino}-1-oxohexan-2-yl]-D-glutamine


Mass: 461.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H31N5O9
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 464 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 18% PEG 3350, 0.1M BISTRIS PROPANE PH7.0, 0.2M POTASSIUM THIOCYANATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0064
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0064 Å / Relative weight: 1
ReflectionResolution: 1.7→47.63 Å / Num. obs: 54041 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 13.1 % / Biso Wilson estimate: 23.57 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 3.14 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.912 Å / SU ML: 0.17 / σ(F): 1.33 / Phase error: 17.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1783 2747 5.1 %
Rwork0.1474 --
obs0.149 54028 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.4 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 66 464 4382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014040
X-RAY DIFFRACTIONf_angle_d1.3685512
X-RAY DIFFRACTIONf_dihedral_angle_d12.7831486
X-RAY DIFFRACTIONf_chiral_restr0.079590
X-RAY DIFFRACTIONf_plane_restr0.007730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72930.26081390.22572492X-RAY DIFFRACTION100
1.7293-1.76080.24191360.21682552X-RAY DIFFRACTION100
1.7608-1.79460.22861200.18832520X-RAY DIFFRACTION100
1.7946-1.83130.22831280.17062563X-RAY DIFFRACTION100
1.8313-1.87110.19021390.16112501X-RAY DIFFRACTION100
1.8711-1.91460.20371470.15692517X-RAY DIFFRACTION100
1.9146-1.96250.1921470.14822520X-RAY DIFFRACTION100
1.9625-2.01560.19881200.14672564X-RAY DIFFRACTION100
2.0156-2.07490.20571330.14952555X-RAY DIFFRACTION100
2.0749-2.14180.21881440.14972520X-RAY DIFFRACTION100
2.1418-2.21840.18381410.14272552X-RAY DIFFRACTION100
2.2184-2.30720.19761260.13762559X-RAY DIFFRACTION100
2.3072-2.41220.19981230.14212577X-RAY DIFFRACTION100
2.4122-2.53940.1791410.14062543X-RAY DIFFRACTION100
2.5394-2.69850.21421390.14982572X-RAY DIFFRACTION100
2.6985-2.90680.17011320.15722583X-RAY DIFFRACTION100
2.9068-3.19920.19151580.15252584X-RAY DIFFRACTION100
3.1992-3.6620.15241150.13742633X-RAY DIFFRACTION100
3.662-4.61310.13841590.1222608X-RAY DIFFRACTION100
4.6131-45.92920.16421600.15732766X-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)
11.64341.2135-0.56762.5361-1.11441.73640.061-0.04380.6547-0.359-0.0135-0.3839-0.5513-0.0611-0.1280.46150.02460.15280.13710.01290.501125.947317.306-41.7299
22.06150.1899-0.80341.45860.56981.84660.0556-0.31820.050.19220.01160.07740.01540.1428-0.09110.14150.01550.00780.1925-0.0320.11914.513-1.0922-16.349
32.62310.5727-0.64542.53460.60652.9385-0.09110.0488-0.36820.120.03420.15020.4971-0.25890.12230.233-0.02090.01890.1709-0.00490.23515.2995-19.7161-25.7389
42.4395-0.4733-1.89672.38252.27225.24030.1682-0.24020.47190.10340.0595-0.0485-0.72810.2439-0.22780.3681-0.05120.03590.2503-0.05650.273921.369611.7907-17.4065
52.0887-0.1526-0.50391.6736-0.25742.44570.1210.17920.4011-0.1170.04870.0874-0.4202-0.0401-0.13540.1840.0050.03630.11510.00710.186526.49497.8596-45.3651
66.16050.2450.19386.89532.47067.5280.3050.7736-0.4736-0.5633-0.04190.0704-0.1634-0.1044-0.24130.20320.0289-0.01270.30260.02150.235733.3760.418-62.6031
72.07910.1295-1.23941.6375-1.21285.53510.2667-0.22060.5675-0.07620.135-0.1834-0.57750.5549-0.30080.3-0.1230.07890.2287-0.08310.381939.256911.8856-42.1601
82.7006-0.4184-1.11861.6091-0.30942.6094-0.0783-0.01570.0907-0.03610.0309-0.0489-0.05150.0590.02950.15930.00310.01350.1233-0.01260.163133.5917-1.7737-45.5676
95.3381-1.9524-0.5663.31071.2161.9605-0.2964-0.44350.1736-0.00690.1892-0.5833-0.08530.75440.07950.16-0.03150.02190.31-0.00810.293647.12550.0102-43.7497
105.68111.28110.17693.33011.48693.1774-0.0194-0.1192-0.55140.33920.0193-0.70880.46520.75510.04690.26490.10230.04690.36240.04890.370650.9815-19.9635-44.0714
113.1652-0.7147-0.98632.5303-0.55382.9944-0.09560.0502-0.3587-0.02420.00430.10580.27520.06130.06460.13810.0150.01590.1261-0.03520.170637.8922-15.5581-46.6044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 17 THROUGH 37 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 38 THROUGH 185 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 186 THROUGH 259 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 17 THROUGH 37 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 38 THROUGH 107 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 108 THROUGH 125 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 126 THROUGH 143 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 144 THROUGH 169 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 170 THROUGH 185 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 186 THROUGH 200 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 201 THROUGH 259 )

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