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- PDB-4oxi: Crystal structure of Vibrio cholerae adenylation domain AlmE in c... -

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Basic information

Entry
Database: PDB / ID: 4oxi
TitleCrystal structure of Vibrio cholerae adenylation domain AlmE in complex with glycyl-adenosine-5'-phosphate
ComponentsEnterobactin synthetase component F-related protein
KeywordsLIGASE / Adenylation domain / Glycine / ATP / Glycyl-adenosine-5'-phosphate
Function / homology
Function and homology information


D-alanine:D-alanyl carrier protein ligase-like / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily ...D-alanine:D-alanyl carrier protein ligase-like / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCYL-ADENOSINE-5'-PHOSPHATE / Enterobactin synthetase component F-related protein
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.261 Å
AuthorsFage, C.D. / Henderson, J.C. / Keatinge-Clay, A.T. / Trent, M.S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106112 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI064184 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI76322 United States
Army Research OfficeW911NF-12-1-0390 United States
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Antimicrobial peptide resistance of Vibrio cholerae results from an LPS modification pathway related to nonribosomal peptide synthetases.
Authors: Henderson, J.C. / Fage, C.D. / Cannon, J.R. / Brodbelt, J.S. / Keatinge-Clay, A.T. / Trent, M.S.
History
DepositionFeb 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords / symmetry
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _symmetry.Int_Tables_number
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enterobactin synthetase component F-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7712
Polymers65,3671
Non-polymers4041
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.039, 116.039, 99.584
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Enterobactin synthetase component F-related protein


Mass: 65366.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_1579 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KRQ7
#2: Chemical ChemComp-GAP / GLYCYL-ADENOSINE-5'-PHOSPHATE


Mass: 404.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N6O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.18 Å3/Da / Density % sol: 61.3 % / Description: Rod-shaped
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 50 mM magnesium chloride, 100 mM HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 36632 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 16.6
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.26-2.3100.9163.618001.497100
2.3-2.3410.30.68218071.348100
2.34-2.3910.40.57818191.211100
2.39-2.4310.40.49717971.18100
2.43-2.4910.50.41518141.125100
2.49-2.5510.60.35418221.11100
2.55-2.6110.60.31817951.081100
2.61-2.6810.60.2918241.396100
2.68-2.7610.70.23518201.026100
2.76-2.8510.80.18618030.929100
2.85-2.9510.90.15918320.861100
2.95-3.07110.12518300.792100
3.07-3.21110.10618210.722100
3.21-3.3811.10.10218270.741100
3.38-3.59110.09818330.857100
3.59-3.8610.20.08418470.81100
3.86-4.2511.10.06818420.69100
4.25-4.8711.10.05118550.406100
4.87-6.1311.10.0518800.389100
6.13-5010.60.04419640.31899.7

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Phasing

PhasingMethod: molecular replacement

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PheA (PDB 1AMU, residues 17-428)

1amu


Resolution: 2.261→37.785 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1927 1829 5 %Random selection
Rwork0.1662 ---
obs0.1676 36586 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 2.261→37.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4214 0 27 157 4398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084343
X-RAY DIFFRACTIONf_angle_d1.0855918
X-RAY DIFFRACTIONf_dihedral_angle_d14.581574
X-RAY DIFFRACTIONf_chiral_restr0.075669
X-RAY DIFFRACTIONf_plane_restr0.005754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2608-2.32190.23761320.20662658X-RAY DIFFRACTION100
2.3219-2.39020.26641380.19812627X-RAY DIFFRACTION100
2.3902-2.46730.29231170.19582663X-RAY DIFFRACTION100
2.4673-2.55550.19741420.18332644X-RAY DIFFRACTION100
2.5555-2.65780.1991150.18582650X-RAY DIFFRACTION100
2.6578-2.77870.21371330.18042680X-RAY DIFFRACTION100
2.7787-2.92510.23551560.18592631X-RAY DIFFRACTION100
2.9251-3.10830.20491500.18542667X-RAY DIFFRACTION100
3.1083-3.34820.18781300.17392668X-RAY DIFFRACTION100
3.3482-3.68490.17311510.16242655X-RAY DIFFRACTION100
3.6849-4.21750.16851550.1492690X-RAY DIFFRACTION100
4.2175-5.31120.17161440.13712722X-RAY DIFFRACTION100
5.3112-37.79050.1751660.15372802X-RAY DIFFRACTION100

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