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- PDB-3hgu: Structure of Phenazine Antibiotic Biosynthesis Protein -

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Basic information

Entry
Database: PDB / ID: 3hgu
TitleStructure of Phenazine Antibiotic Biosynthesis Protein
ComponentsEhpF
KeywordsBIOSYNTHETIC PROTEIN / Phenazine / Antibiotic
Function / homologyANL, N-terminal domain / EhpF
Function and homology information
Biological speciesPantoea agglomerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsBera, A.K. / Atanasova, V. / Parsons, J.F.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2010
Title: Structure of the D-alanylgriseoluteic acid biosynthetic protein EhpF, an atypical member of the ANL superfamily of adenylating enzymes.
Authors: Bera, A.K. / Atanasova, V. / Gamage, S. / Robinson, H. / Parsons, J.F.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EhpF
B: EhpF


Theoretical massNumber of molelcules
Total (without water)82,3712
Polymers82,3712
Non-polymers00
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-9 kcal/mol
Surface area30080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.854, 89.854, 188.557
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 EhpF


Mass: 41185.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pantoea agglomerans (bacteria) / Gene: ehpF / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GPH0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 1M K-Na Tartrate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979099
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979099 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 65275 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 15.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 55.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 5.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.927 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3289 5.1 %RANDOM
Rwork0.193 ---
obs0.196 61712 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5498 0 0 394 5892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225672
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9557727
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8985709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34323.802263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99315942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6291542
X-RAY DIFFRACTIONr_chiral_restr0.1010.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024345
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.22678
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23886
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2390
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3891.53583
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.22725699
X-RAY DIFFRACTIONr_scbond_it3.22732355
X-RAY DIFFRACTIONr_scangle_it4.6574.52020
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→1.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 236 -
Rwork0.22 4488 -
obs--99.39 %

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