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- PDB-4aey: Crystal structure of FolX from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4aey
TitleCrystal structure of FolX from Pseudomonas aeruginosa
ComponentsD-ERYTHRO-7,8-DIHYDRONEOPTERIN TRIPHOSPHATE EPIMERASE
KeywordsISOMERASE / PTERIDINE BIOSYNTHESIS
Function / homology
Function and homology information


dihydroneopterin triphosphate 2'-epimerase activity / dihydroneopterin aldolase activity / folic acid-containing compound metabolic process / tetrahydrobiopterin biosynthetic process / cytoplasm / cytosol
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
D-erythro-7,8-dihydroneopterin triphosphate epimerase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGabrielsen, M. / Beckham, K.S.H. / Roe, A.J.
CitationJournal: FEBS Lett. / Year: 2012
Title: Folx from Pseudomonas Aeruginosa is Octameric in Both Crystal and Solution.
Authors: Gabrielsen, M. / Beckham, K.S.H. / Cogdell, R.J. / Byron, O. / Roe, A.J.
History
DepositionJan 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Other
Revision 1.2May 23, 2012Group: Other
Revision 1.3Jun 20, 2012Group: Other
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-ERYTHRO-7,8-DIHYDRONEOPTERIN TRIPHOSPHATE EPIMERASE


Theoretical massNumber of molelcules
Total (without water)18,0121
Polymers18,0121
Non-polymers00
Water1448
1
A: D-ERYTHRO-7,8-DIHYDRONEOPTERIN TRIPHOSPHATE EPIMERASE
x 8


Theoretical massNumber of molelcules
Total (without water)144,0948
Polymers144,0948
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_556-y,-x,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area15530 Å2
ΔGint-97.9 kcal/mol
Surface area51170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.980, 133.980, 133.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein D-ERYTHRO-7,8-DIHYDRONEOPTERIN TRIPHOSPHATE EPIMERASE / 7 / 8-DIHYDRONEOPTERIN-TRIPHOSPHATE-EPIMERASE


Mass: 18011.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYG7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN HAS AN N-TERMINAL HIS-TAG AND TEV CLEAVAGE SITE

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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: 2.78 Å3/Da / Density % sol: 55.78 % / Description: NONE
Crystal growDetails: 40 % (V/V) 1,2-PROPANEDIOL, 100 MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3→97.74 Å / Num. obs: 4383 / % possible obs: 100 % / Observed criterion σ(I): 2.5 / Redundancy: 23.7 % / Biso Wilson estimate: 123.56 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 25.1 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B9L

1b9l


Resolution: 3→66.99 Å / Cor.coef. Fo:Fc: 0.9047 / Cor.coef. Fo:Fc free: 0.878 / SU R Cruickshank DPI: 0.64 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.703 / SU Rfree Blow DPI: 0.393 / SU Rfree Cruickshank DPI: 0.388
Details: RESIDUES 1-5 AND 47-54 ARE DISORDERED. IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM 1B9L_MONO_CHAINSAW1.PDB
RfactorNum. reflection% reflectionSelection details
Rfree0.3107 203 4.6 %RANDOM
Rwork0.283 ---
obs0.2843 4382 100 %-
Displacement parametersBiso mean: 133.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→66.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms754 0 0 8 762
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01765HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.331039HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d245SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes17HARMONIC2
X-RAY DIFFRACTIONt_gen_planes116HARMONIC5
X-RAY DIFFRACTIONt_it765HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion21.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion110SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact835SEMIHARMONIC4
LS refinement shellResolution: 3→3.35 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3573 58 4.81 %
Rwork0.258 1148 -
all0.2623 1206 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 12.9782 Å / Origin y: 13.4566 Å / Origin z: 52.8251 Å
111213212223313233
T-0.2648 Å2-0.1121 Å2-0.152 Å2--0.304 Å20.152 Å2--0.304 Å2
L0 °2-0.9399 °21.1538 °2-7.4346 °2-1.4956 °2--3.4971 °2
S-0.1098 Å °0.5442 Å °0.2497 Å °-0.5442 Å °-0.3246 Å °-0.2767 Å °-0.5366 Å °0.521 Å °0.4344 Å °
Refinement TLS groupSelection details: (CHAIN A)

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