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- PDB-7su7: Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystall... -

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Basic information

Entry
Database: PDB / ID: 7su7
TitleDihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with product
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
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 speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBourne, C.R.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103447
CitationJournal: To Be Published
Title: Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with product
Authors: Bourne, C.R.
History
DepositionNov 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)65,98413
Polymers64,5974
Non-polymers1,3879
Water5,981332
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)131,96826
Polymers129,1938
Non-polymers2,77518
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area26390 Å2
ΔGint-85 kcal/mol
Surface area36820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.524, 81.185, 96.249
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-378-

HOH

21D-384-

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: pMSCG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BS21(DE3) / References: UniProt: Q8CZR7, dihydroneopterin aldolase
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-PH2 / 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE


Mass: 195.179 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H9N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 - 0.1M BisTris, 0.1-0.2 M CaCl2, 0 - 0.1M NaCl, 43 - 49% MPD
PH range: 6.2 - 6.7

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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: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 41395 / % possible obs: 99.4 % / Redundancy: 4.1 %
Details: Only reflections up to 2.09 A were used for refinement. The Rmerge using a 2.09 A high resolution cutoff is 0.213
Rmerge(I) obs: 0.268 / Rpim(I) all: 0.148 / Rrim(I) all: 0.307 / Χ2: 2.317 / Net I/σ(I): 3.1 / Num. measured all: 171031
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.983.21.520010.3310.951.7841.03495.9
1.98-2.023.71.14319990.3870.6751.3331.11399.2
2.02-2.0640.99720320.4690.5621.1481.10298.3
2.06-2.14.10.94820500.4830.5331.0921.26298.6
2.1-2.154.20.89320210.5310.4951.0241.22699.5
2.15-2.24.20.70620410.5830.3910.8091.32699.2
2.2-2.254.30.68920410.6180.3780.7881.34399.3
2.25-2.314.30.64920400.6680.3540.7411.5499.7
2.31-2.384.40.55420750.6550.2980.631.681100
2.38-2.464.50.55220660.7230.2940.6271.605100
2.46-2.544.50.48920600.8010.2610.5561.788100
2.54-2.654.50.39220560.8310.2090.4451.989100
2.65-2.774.40.36420720.8580.1950.4142.048100
2.77-2.914.40.29920790.8950.1610.342.259100
2.91-3.14.30.23520810.9230.1270.2682.608100
3.1-3.334.30.18320790.9490.10.2092.836100
3.33-3.674.20.15221040.9720.0830.1743.8499.7
3.67-4.240.14621230.9750.0810.1684.81899.8
4.2-5.293.80.11621250.9810.0660.1345.25199.6
5.29-503.30.09822500.9770.0580.1156.16798.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ojo

6ojo


Resolution: 2.09→41.4 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 1995 6.02 %
Rwork0.1792 31121 -
obs0.1825 33116 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.93 Å2 / Biso mean: 28.3816 Å2 / Biso min: 8.39 Å2
Refinement stepCycle: final / Resolution: 2.09→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 96 332 4136
Biso mean--34.14 34.83 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093888
X-RAY DIFFRACTIONf_angle_d0.925271
X-RAY DIFFRACTIONf_dihedral_angle_d20.5051414
X-RAY DIFFRACTIONf_chiral_restr0.067593
X-RAY DIFFRACTIONf_plane_restr0.005672
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 (%)
2.09-2.140.26621320.22222056218892
2.14-2.20.26641380.20722168230698
2.2-2.270.28781400.21072193233398
2.27-2.340.28311410.21392192233398
2.34-2.420.26751420.21452208235098
2.42-2.520.30331420.20942209235199
2.52-2.630.24271430.19842231237499
2.63-2.770.26091440.19332239238399
2.77-2.950.27651440.18472238238299
2.95-3.180.23291420.17562249239199
3.18-3.490.20191460.1682257240399
3.49-40.20471440.15162252239698
4-5.040.20921460.14492269241597
5.04-41.40.20611510.18062360251197

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