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- PDB-7su8: DIHYDRONEOPTERIN ALDOLASE (DHNA) FROM YERSINIA PESTIS with alkyla... -

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Basic information

Entry
Database: PDB / ID: 7su8
TitleDIHYDRONEOPTERIN ALDOLASE (DHNA) FROM YERSINIA PESTIS with alkylated Cys50 CO-CRYSTALLIZED with 7,8-dihydroneopterin
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
1-ETHYL-PYRROLIDINE-2,5-DIONE / Chem-PH2 / 7,8-dihydroneopterin aldolase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 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 with alkylated Cys50 CO-CRYSTALLIZED with 7,8-dihydroneopterin
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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)33,3019
Polymers32,2982
Non-polymers1,0037
Water1,08160
1
B: 7,8-dihydroneopterin aldolase
hetero molecules

B: 7,8-dihydroneopterin aldolase
hetero molecules

B: 7,8-dihydroneopterin aldolase
hetero molecules

B: 7,8-dihydroneopterin aldolase
hetero molecules

A: 7,8-dihydroneopterin aldolase
hetero molecules

A: 7,8-dihydroneopterin aldolase
hetero molecules

A: 7,8-dihydroneopterin aldolase
hetero molecules

A: 7,8-dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,20636
Polymers129,1938
Non-polymers4,01328
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
crystal symmetry operation5_444x-1/2,y-1/2,z-1/21
crystal symmetry operation6_444-x-1/2,-y-1/2,z-1/21
crystal symmetry operation7_444-y-1/2,x-1/2,z-1/21
crystal symmetry operation8_444y-1/2,-x-1/2,z-1/21
Buried area28380 Å2
ΔGint-71 kcal/mol
Surface area37890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.604, 72.604, 105.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 7,8-dihydroneopterin aldolase


Mass: 16149.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: y3531 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8CZR7, dihydroneopterin aldolase

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Non-polymers , 5 types, 67 molecules

#2: Chemical ChemComp-NEN / 1-ETHYL-PYRROLIDINE-2,5-DIONE


Mass: 127.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PH2 / 2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE


Mass: 195.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 43.1 %
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: May 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 7332 / % possible obs: 91.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.025 / Rrim(I) all: 0.05 / Χ2: 0.55 / Net I/σ(I): 9.7 / Num. measured all: 25781
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.72.50.2063700.9430.1410.2520.53490.7
2.7-2.742.80.1673780.960.1090.2010.46694.3
2.74-2.83.10.1783860.9490.1130.2130.57395.1
2.8-2.853.30.1693610.9610.1020.1990.54993.5
2.85-2.923.30.1623730.9590.0980.1910.53694
2.92-2.983.50.1053580.9880.0610.1220.47194
2.98-3.063.40.1053900.9890.0630.1230.53593.5
3.06-3.143.60.093630.990.0530.1050.44293.6
3.14-3.233.70.0763680.9920.0430.0880.51493.6
3.23-3.343.70.0623760.9960.0350.0720.50292.4
3.34-3.463.80.0543700.9960.030.0620.58192.7
3.46-3.63.80.0523590.9970.0280.0590.50392.5
3.6-3.763.80.0433640.9970.0230.0490.50791.9
3.76-3.963.90.0363750.9980.0190.0410.50691.7
3.96-4.213.80.0353560.9990.0190.040.56990.4
4.21-4.533.80.0293720.9990.0160.0340.58291.4
4.53-4.993.80.0283410.9990.0160.0320.56189
4.99-5.713.80.0293670.9990.0160.0330.56289.5
5.71-7.193.70.0323550.9990.0180.0370.62687
7.19-503.50.0263500.9990.0160.0310.88885.2

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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: 2.65→36.87 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 722 9.86 %
Rwork0.2054 6601 -
obs0.2109 7323 91.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.37 Å2 / Biso mean: 53.2409 Å2 / Biso min: 19.89 Å2
Refinement stepCycle: final / Resolution: 2.65→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 70 60 1940
Biso mean--70.23 49.67 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061927
X-RAY DIFFRACTIONf_angle_d0.9422611
X-RAY DIFFRACTIONf_dihedral_angle_d17.332698
X-RAY DIFFRACTIONf_chiral_restr0.061296
X-RAY DIFFRACTIONf_plane_restr0.003330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.860.36121580.25161337149593
2.86-3.150.3341420.2471330147294
3.15-3.60.28011370.21591343148093
3.6-4.540.22821420.17951316145891
4.54-36.870.2141430.19211275141888

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