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- PDB-6ojo: Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystall... -

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Basic information

Entry
Database: PDB / ID: 6ojo
TitleDihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with pterine
Components7,8-dihydroneopterin aldolase
KeywordsBIOSYNTHETIC PROTEIN / folB folate pathway
Function / homology
Function and homology information


dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / cytoplasm
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PTERINE / 7,8-dihydroneopterin aldolase / 7,8-dihydroneopterin aldolase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.886 Å
AuthorsBourne, C.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1359457 United States
CitationJournal: To Be Published
Title: Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with pterine
Authors: Bourne, C.R.
History
DepositionApr 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
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: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
C: 7,8-dihydroneopterin aldolase
D: 7,8-dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2498
Polymers64,5974
Non-polymers6534
Water7,873437
1
A: 7,8-dihydroneopterin aldolase
B: 7,8-dihydroneopterin aldolase
C: 7,8-dihydroneopterin aldolase
D: 7,8-dihydroneopterin aldolase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)130,49816
Polymers129,1938
Non-polymers1,3058
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area21660 Å2
ΔGint-81 kcal/mol
Surface area37900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.086, 81.489, 96.624
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-401-

HOH

21C-407-

HOH

31D-398-

HOH

41D-407-

HOH

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Components

#1: Protein
7,8-dihydroneopterin aldolase


Mass: 16149.166 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: y3531 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8CZR7, UniProt: A0A5P8YJX5*PLUS, dihydroneopterin aldolase
#2: Chemical
ChemComp-PE0 / PTERINE


Mass: 163.137 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 43.22 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BisTris pH 6.5 0.2 M CaCl2 0.05 M NaCl 47% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.886→41.557 Å / Num. obs: 45556 / % possible obs: 99 % / Redundancy: 4.2 % / Biso Wilson estimate: 19.45 Å2 / Rrim(I) all: 0.11 / Net I/σ(I): 15.5
Reflection shellResolution: 1.886→1.954 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4210 / Rrim(I) all: 0.584 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r2e

3r2e


Resolution: 1.886→41.557 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.27
RfactorNum. reflection% reflection
Rfree0.2065 2000 4.4 %
Rwork0.1841 --
obs0.1851 45479 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.29 Å2 / Biso mean: 22.2082 Å2 / Biso min: 8.47 Å2
Refinement stepCycle: final / Resolution: 1.886→41.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 48 437 4189
Biso mean--16.79 33.55 -
Num. residues----470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.886-1.93280.271280.25462796292489
1.9328-1.9850.2691390.21193025316498
1.985-2.04340.22171420.23079322199
2.0434-2.10940.24041410.199730833224100
2.1094-2.18480.22281420.193130933235100
2.1848-2.27230.20811430.184831083251100
2.2723-2.37570.2221430.188831203263100
2.3757-2.50090.21211440.194731273271100
2.5009-2.65760.22381420.186131063248100
2.6576-2.86270.19231450.181831453290100
2.8627-3.15070.19871450.180131483293100
3.1507-3.60640.18471450.1631593304100
3.6064-4.54280.1571470.159732043351100
4.5428-41.56750.23461540.19333286344098

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