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- PDB-8su7: Crystal structure of Bacillus anthracis dihydroneopterin aldolase -

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Basic information

Entry
Database: PDB / ID: 8su7
TitleCrystal structure of Bacillus anthracis dihydroneopterin aldolase
Components7,8-dihydroneopterin aldolase
KeywordsLYASE / dihydroneopterin aldolase / DHNA
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
7,8-dihydroneopterin aldolase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Authors: Shaw, G.X. / Li, Y. / Yan, H. / Ji, X.
History
DepositionMay 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1144
Polymers27,9902
Non-polymers1242
Water97354
1
A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
hetero molecules

A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
hetero molecules

A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
hetero molecules

A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,45616
Polymers111,9598
Non-polymers4978
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area24520 Å2
ΔGint-57 kcal/mol
Surface area36610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.712, 63.712, 134.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein 7,8-dihydroneopterin aldolase


Mass: 13994.912 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: CHO2Na, PEG3350, Ethylene glycol, 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
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 9468 / % possible obs: 90.2 % / Redundancy: 4.8 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.02 / Rrim(I) all: 0.045 / Χ2: 0.966 / Net I/σ(I): 17.2 / Num. measured all: 45448
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.494.50.1427610.9870.9970.0690.1590.98673.7
2.49-2.594.60.1038020.9920.9980.050.1150.96675.5
2.59-2.74.80.1018330.9940.9980.0490.1120.94579.6
2.7-2.854.80.0838640.9970.9990.0410.0930.94184.4
2.85-3.024.80.07410000.9960.9990.0370.0830.95793.8
3.02-3.264.90.05510420.9980.9990.0280.0610.96699
3.26-3.5850.04110340.99910.020.0460.99399.3
3.58-4.14.90.03110380.99910.0160.0351.00399.1
4.1-5.164.80.02710350.99910.0140.0310.98198.3
5.16-304.90.03410590.9970.9990.0180.0380.91998.4

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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: 5F3M

5f3m


Resolution: 2.4→28.8 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 36.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 948 10.03 %Random selection
Rwork0.2211 ---
obs0.2266 9449 90.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 8 54 2028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062012
X-RAY DIFFRACTIONf_angle_d0.7532712
X-RAY DIFFRACTIONf_dihedral_angle_d17.739778
X-RAY DIFFRACTIONf_chiral_restr0.062296
X-RAY DIFFRACTIONf_plane_restr0.005352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.530.33521080.2777992X-RAY DIFFRACTION73
2.53-2.690.36621170.25671053X-RAY DIFFRACTION79
2.69-2.890.40981250.27271151X-RAY DIFFRACTION85
2.89-3.180.32641450.26091302X-RAY DIFFRACTION97
3.19-3.650.28311510.24891327X-RAY DIFFRACTION99
3.65-4.590.23491530.19111325X-RAY DIFFRACTION99
4.59-28.80.24051490.18921351X-RAY DIFFRACTION98

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