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- PDB-3v9o: Crystal structure of Dihydroneopterin aldolase (BTH_I0291) from B... -

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Basic information

Entry
Database: PDB / ID: 3v9o
TitleCrystal structure of Dihydroneopterin aldolase (BTH_I0291) from Burkholderia thailendensis bound to guanine.
ComponentsDihydroneopterin aldolase
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Dihydroneopterin aldolase / Dihydroneopterin
Function / homology
Function and homology information


dihydroneopterin aldolase activity / folic acid-containing compound metabolic process / queuosine biosynthetic process / oxidoreductase activity
Similarity search - Function
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
GUANINE / Dihydroneopterin aldolase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionDec 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5688
Polymers16,0101
Non-polymers5587
Water1,69394
1
A: Dihydroneopterin aldolase
hetero molecules

A: Dihydroneopterin aldolase
hetero molecules

A: Dihydroneopterin aldolase
hetero molecules

A: Dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,27132
Polymers64,0414
Non-polymers2,23028
Water724
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 area15500 Å2
ΔGint7 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.984, 73.984, 110.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-232-

HOH

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Components

#1: Protein Dihydroneopterin aldolase /


Mass: 16010.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I0291 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T1V0
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GUN / GUANINE / Guanine


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 M ammonium sulfate, 0.2 M lithium sulfate, 0.1 M TRIS, SSGCID: ButhA.17925.a.A1 PW33456, VAPOR DIFFUSION, SITTING DROP, temperature 289K, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 27570 / % possible obs: 99.9 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.061 / Χ2: 1.016 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.45-1.4814.40.55913511.011100
1.48-1.514.30.45913501.0261100
1.5-1.5314.40.40813531.0231100
1.53-1.5614.40.33413631.0161100
1.56-1.614.40.27213601.0061100
1.6-1.6314.40.23813571.0111100
1.63-1.6714.50.20813401.0261100
1.67-1.7214.40.1713821.0111100
1.72-1.7714.50.147138811100
1.77-1.8314.50.11813350.9541100
1.83-1.8914.40.113610.9751100
1.89-1.9714.40.08913720.9681100
1.97-2.0614.40.07713860.9791100
2.06-2.1714.40.07513711.0031100
2.17-2.3140.07813821.0081100
2.3-2.4813.20.07613921.0771100
2.48-2.7312.90.07213941.0521100
2.73-3.1213.40.06414040.9871100
3.12-3.9413.70.04514281.057199.9
3.94-5013.30.04215011.145198.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3O1K

3o1k


Resolution: 1.451→38.064 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8883 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 17.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 1390 5.04 %Random
Rwork0.1736 ---
all0.2044 28959 --
obs0.1752 27569 99.91 %-
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.968 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso max: 100 Å2 / Biso mean: 26.1951 Å2 / Biso min: 11.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.3429 Å2-0 Å20 Å2
2---1.3429 Å2-0 Å2
3---2.6857 Å2
Refinement stepCycle: LAST / Resolution: 1.451→38.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 36 94 1075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191039
X-RAY DIFFRACTIONf_angle_d1.8121411
X-RAY DIFFRACTIONf_chiral_restr0.104165
X-RAY DIFFRACTIONf_plane_restr0.01181
X-RAY DIFFRACTIONf_dihedral_angle_d13.669396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4514-1.50330.25481300.23825672697100
1.5033-1.56340.22341310.209625862717100
1.5634-1.63460.18981310.183425852716100
1.6346-1.72080.20871540.170825722726100
1.7208-1.82860.21081270.160425962723100
1.8286-1.96980.19561420.165425912733100
1.9698-2.1680.19441640.163925932757100
2.168-2.48160.19361490.166426252774100
2.4816-3.12640.21531390.178826562795100
3.1264-38.07750.20421230.17222808293199
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)
18.28392.6737-2.6561.83791.69497.533-0.0624-1.57250.10631.72970.2701-0.7351-0.65390.2299-0.15521.29590.1322-0.22130.58950.04950.539427.8882-36.919431.712
22.831.689-1.8796.5733-4.06784.14660.0181-0.0438-0.02350.1632-0.1663-0.1417-0.16950.18840.14720.0934-0.0089-0.01720.1481-0.0290.068924.4878-29.529214.7117
33.4591.1479-1.03052.7113-1.16412.40120.0612-0.03320.00790.19480.06860.3465-0.1154-0.1958-0.10940.11850.02980.03330.1171-0.01670.112217.7808-32.79317.0526
43.35790.1280.06164.2348-5.57387.3601-0.1353-0.0480.17640.00130.50090.6222-0.0294-0.3629-0.42730.14490.0219-0.00040.20590.00990.177616.8776-23.606514.1401
57.34861.42540.54827.1343-3.16441.94790.0297-0.614-0.03021.295-0.6114-1.6183-0.64430.51660.50270.4906-0.0051-0.13730.36740.14790.630118.9067-11.268512.3367
65.3220.9503-3.14480.8575-0.48512.50590.0163-0.02370.07870.0714-0.03740.0721-0.0276-0.05130.02930.14150.0093-0.00320.1114-0.01960.084228.5596-21.913217.0647
76.4531-3.71-1.38876.3210.59952.1628-0.0371-1.09050.1141.12840.04380.07190.2331-0.05860.04590.2888-0.04910.03410.3645-0.06090.120224.4168-25.545530.5617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 10:14)A10 - 14
2X-RAY DIFFRACTION2(chain A and resid 15:33)A15 - 33
3X-RAY DIFFRACTION3(chain A and resid 34:72)A34 - 72
4X-RAY DIFFRACTION4(chain A and resid 73:82)A73 - 82
5X-RAY DIFFRACTION5(chain A and resid 83:86)A83 - 86
6X-RAY DIFFRACTION6(chain A and resid 87:131)A87 - 131
7X-RAY DIFFRACTION7(chain A and resid 132:136)A132 - 136

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