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- PDB-8sv5: Crystal structure of Bacillus anthracis dihydroneopterin aldolase... -

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Basic information

Entry
Database: PDB / ID: 8sv5
TitleCrystal structure of Bacillus anthracis dihydroneopterin aldolase in complex with 6-hydroxymethyl-7,8-dihydropterin
Components7,8-dihydroneopterin aldolase
KeywordsLYASE / dihydroneopterin aldolase / DHNA / 6-hydroxymethyl-7 / 8-dihydropterin / product / product complex
Function / homology
Function and homology information


dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / cytoplasm
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Domain/homology
Chem-PH2 / 7,8-dihydroneopterin aldolase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsShaw, G.X. / Li, Y. / Yan, H. / Ji, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To be published
Title: Crystal structure of Bacillus anthracis dihydroneopterin aldolase in complex with 6-hydroxymethyl-7,8-dihydropterin
Authors: Shaw, G.X. / Li, Y. / Yan, H. / Ji, X.
History
DepositionMay 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
C: 7,8-dihydroneopterin aldolase
D: 7,8-dihydroneopterin aldolase
E: 7,8-dihydroneopterin aldolase
F: 7,8-dihydroneopterin aldolase
G: 7,8-dihydroneopterin aldolase
H: 7,8-dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,64518
Polymers111,9598
Non-polymers1,68610
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Bacillus anthracis dihydroneopterin aldolase in complex with 6-hydroxymethyl-7,8-dihydropterin
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26780 Å2
ΔGint-65 kcal/mol
Surface area36080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.421, 101.849, 77.204
Angle α, β, γ (deg.)90.00, 101.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
7,8-dihydroneopterin aldolase


Mass: 13994.912 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: folB, GBAA_0072 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L7HSV1, dihydroneopterin aldolase
#2: Chemical
ChemComp-PH2 / 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE


Mass: 195.179 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H9N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium acetate, cacodylate, etc.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 27, 2006 / Details: Double crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 49567 / % possible obs: 96.3 % / Redundancy: 3.5 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.065 / Rrim(I) all: 0.133 / Χ2: 0.953 / Net I/σ(I): 7.7 / Num. measured all: 173082
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.15-2.231.70.74240090.4680.7980.6240.9750.9478.7
2.23-2.3220.65345850.5690.8510.5160.8370.97489.1
2.32-2.422.50.63549520.6450.8860.4540.7850.9796.2
2.42-2.553.20.5750890.7190.9140.3670.680.9799.5
2.55-2.713.90.46351440.8430.9560.2670.5360.957100
2.71-2.924.20.33751150.9190.9790.1860.3850.944100
2.92-3.214.30.21551270.9640.9910.1170.2450.95699.9
3.21-3.674.20.1251500.9840.9960.0660.1370.96599.7
3.67-4.634.20.0751620.9930.9980.0390.080.9899.8
4.63-304.20.07152340.9940.9980.0380.0810.89699.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8SU7

8su7


Resolution: 2.16→29.88 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1999 4.04 %Random selection
Rwork0.1807 ---
obs0.1826 49504 95.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7864 0 120 183 8167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038150
X-RAY DIFFRACTIONf_angle_d0.63111004
X-RAY DIFFRACTIONf_dihedral_angle_d18.573146
X-RAY DIFFRACTIONf_chiral_restr0.061184
X-RAY DIFFRACTIONf_plane_restr0.0061416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.210.37121070.30632549X-RAY DIFFRACTION72
2.21-2.270.33511260.28012978X-RAY DIFFRACTION84
2.27-2.340.36591350.27013225X-RAY DIFFRACTION92
2.34-2.420.33551430.24813382X-RAY DIFFRACTION96
2.42-2.50.27361470.24053501X-RAY DIFFRACTION99
2.5-2.60.27381480.21533514X-RAY DIFFRACTION100
2.6-2.720.27011490.19993543X-RAY DIFFRACTION100
2.72-2.860.26061480.18663511X-RAY DIFFRACTION100
2.86-3.040.21841490.19113536X-RAY DIFFRACTION100
3.04-3.280.25061480.18423522X-RAY DIFFRACTION100
3.28-3.610.22751490.16753537X-RAY DIFFRACTION100
3.61-4.130.19741480.15353546X-RAY DIFFRACTION100
4.13-5.20.17411500.14193557X-RAY DIFFRACTION100
5.2-29.880.19261520.1743604X-RAY DIFFRACTION100

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