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- PDB-6dan: PhdJ WT 2 Angstroms resolution -

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Basic information

Entry
Database: PDB / ID: 6dan
TitlePhdJ WT 2 Angstroms resolution
ComponentsPhdJ
KeywordsLYASE / aldolase / PhdJ
Function / homologyDapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel / lyase activity / PhdJ
Function and homology information
Biological speciesMycobacterium vanbaalenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.047 Å
AuthorsMedellin, B.P. / LeVieux, J.A. / Zhang, Y.J. / Whitman, C.P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-41239 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-104896 United States
Robert A. Welch FoundationF-1334 United States
Robert A. Welch FoundationF-1778 United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural Characterization of the Hydratase-Aldolases, NahE and PhdJ: Implications for the Specificity, Catalysis, and N-Acetylneuraminate Lyase Subgroup of the Aldolase Superfamily.
Authors: LeVieux, J.A. / Medellin, B. / Johnson Jr., W.H. / Erwin, K. / Li, W. / Johnson, I.A. / Zhang, Y.J. / Whitman, C.P.
History
DepositionMay 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PhdJ
B: PhdJ
C: PhdJ
D: PhdJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1946
Polymers144,1234
Non-polymers712
Water13,097727
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-71 kcal/mol
Surface area42860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.406, 136.946, 88.264
Angle α, β, γ (deg.)90.00, 99.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PhdJ


Mass: 36030.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium vanbaalenii (bacteria) / Gene: phdJ / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress / References: UniProt: Q6H2K0
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M MES at pH 7-7.5 and 22-25% in PEG 3350 / PH range: 7-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 72626 / % possible obs: 94.3 % / Redundancy: 3.38 % / Net I/σ(I): 11
Reflection shellResolution: 2→2.12 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.047→39.9 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.08
RfactorNum. reflection% reflection
Rfree0.221 7157 9.85 %
Rwork0.176 --
obs0.18 72626 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.047→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9871 0 2 727 10600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710122
X-RAY DIFFRACTIONf_angle_d0.79813824
X-RAY DIFFRACTIONf_dihedral_angle_d3.4927046
X-RAY DIFFRACTIONf_chiral_restr0.051564
X-RAY DIFFRACTIONf_plane_restr0.0051819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.047-2.07080.28192000.23651780X-RAY DIFFRACTION77
2.0708-2.09520.29732040.23761906X-RAY DIFFRACTION82
2.0952-2.12080.30382250.22522004X-RAY DIFFRACTION87
2.1208-2.14760.27922060.21992052X-RAY DIFFRACTION89
2.1476-2.17590.30052160.21632085X-RAY DIFFRACTION89
2.1759-2.20570.2882200.21132099X-RAY DIFFRACTION91
2.2057-2.23720.29342520.20552132X-RAY DIFFRACTION93
2.2372-2.27060.26792080.20842187X-RAY DIFFRACTION92
2.2706-2.3060.26422550.19682170X-RAY DIFFRACTION96
2.306-2.34380.25132550.19832195X-RAY DIFFRACTION96
2.3438-2.38420.26392490.20422281X-RAY DIFFRACTION95
2.3842-2.42760.24862520.20022202X-RAY DIFFRACTION98
2.4276-2.47430.26682480.19672234X-RAY DIFFRACTION97
2.4743-2.52480.24542470.18172256X-RAY DIFFRACTION97
2.5248-2.57970.25242640.19452258X-RAY DIFFRACTION98
2.5797-2.63970.23672440.17742214X-RAY DIFFRACTION96
2.6397-2.70570.21992690.18182233X-RAY DIFFRACTION98
2.7057-2.77880.23992430.18232229X-RAY DIFFRACTION96
2.7788-2.86050.22052190.18452256X-RAY DIFFRACTION97
2.8605-2.95290.2312490.18032218X-RAY DIFFRACTION96
2.9529-3.05840.25352490.19152229X-RAY DIFFRACTION96
3.0584-3.18080.21942410.17662211X-RAY DIFFRACTION96
3.1808-3.32540.23812230.17592247X-RAY DIFFRACTION95
3.3254-3.50070.21392460.17972178X-RAY DIFFRACTION94
3.5007-3.71990.17912310.1632220X-RAY DIFFRACTION95
3.7199-4.00680.18292400.15382225X-RAY DIFFRACTION95
4.0068-4.40960.18462420.14272256X-RAY DIFFRACTION97
4.4096-5.04660.17812440.13962277X-RAY DIFFRACTION98
5.0466-6.3540.18252650.16312323X-RAY DIFFRACTION100
6.354-39.9110.19392510.16292312X-RAY DIFFRACTION98

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