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- PDB-3r2e: Dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimer... -

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Basic information

Entry
Database: PDB / ID: 3r2e
TitleDihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase from Yersinia pestis.
ComponentsDihydroneopterin aldolase
KeywordsLYASE / structural genomics / IDP90567 / Center for Structural Genomics of Infectious Diseases / CSGID / bifunctional / dihydroneopterin aldolase / dihydroneopterin triphosphate 2'-epimerase
Function / homology
Function and homology information


dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / isomerase activity / tetrahydrofolate biosynthetic process / 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
7,8-dihydroneopterin aldolase / 7,8-dihydroneopterin aldolase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsOsipiuk, J. / Maltseva, N. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase from Yersinia pestis
Authors: Osipiuk, J. / Maltseva, N. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroneopterin aldolase


Theoretical massNumber of molelcules
Total (without water)16,1491
Polymers16,1491
Non-polymers00
Water19811
1
A: Dihydroneopterin aldolase
x 8


Theoretical massNumber of molelcules
Total (without water)129,1938
Polymers129,1938
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area17530 Å2
ΔGint-82 kcal/mol
Surface area40290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.716, 71.716, 107.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Dihydroneopterin aldolase


Mass: 16149.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO-92 / Gene: folB, YPO0648 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0WJ22, UniProt: A0A5P8YJX5*PLUS, dihydroneopterin aldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M calcium chloride, 0.1 M Bis-tris buffer, 45% MPD, 10 mM guanine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 24, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→31 Å / Num. all: 7990 / Num. obs: 7990 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 57.7 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.595 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.15-2.195.80.8552.053951.183100
2.19-2.236.20.7033871.192100
2.23-2.2770.8273921.208100
2.27-2.3270.6924051.311100
2.32-2.377.20.5793721.375100
2.37-2.4270.5664031.279100
2.42-2.4870.4653881.407100
2.48-2.557.10.3673971.359100
2.55-2.6270.3083901.51100
2.62-2.7170.2273911.511100
2.71-2.817.10.1884011.549100
2.81-2.9270.1713921.624100
2.92-3.0570.1213971.90299.7
3.05-3.216.90.0894041.835100
3.21-3.416.90.0684012.01399.8
3.41-3.686.90.0554032.05499.8
3.68-4.056.80.0444081.997100
4.05-4.636.70.0374142.01998.6
4.63-5.836.70.0324071.6699
5.83-505.90.0324431.79495.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O90

2o90


Resolution: 2.15→31 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 16.998 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 368 4.6 %RANDOM
Rwork0.2153 ---
all0.2171 7960 --
obs0.2171 7960 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 157.66 Å2 / Biso mean: 67.9161 Å2 / Biso min: 33.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.15→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 0 11 933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022943
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9371279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8815118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24824.89447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.88915167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.711157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02711
X-RAY DIFFRACTIONr_mcbond_it0.9271.5582
X-RAY DIFFRACTIONr_mcangle_it1.7232942
X-RAY DIFFRACTIONr_scbond_it2.6483361
X-RAY DIFFRACTIONr_scangle_it4.4454.5336
LS refinement shellResolution: 2.15→2.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 27 -
Rwork0.298 540 -
all-567 -
obs-567 98.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.6459-2.6312-7.51486.96144.069211.2237-0.0337-0.80360.31040.19950.2334-0.418-0.17690.6606-0.19960.4312-0.0477-0.1380.4247-0.04430.339711.507413.102912.9308
26.749-1.3949-2.09745.90030.53686.91680.0649-0.55560.7890.4735-0.0484-0.5696-0.5480.5993-0.01640.2696-0.0984-0.11520.2822-0.20430.34316.654716.813115.0975
33.4716-1.9178-0.222214.10557.88516.1364-0.3046-0.61170.30550.00360.0914-0.0198-0.11710.35830.21330.2652-0.0262-0.14110.3899-0.03270.264212.85016.856116.5528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 47
2X-RAY DIFFRACTION2A48 - 85
3X-RAY DIFFRACTION3A86 - 116

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