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- PDB-1b9l: 7,8-DIHYDRONEOPTERIN TRIPHOSPHATE EPIMERASE -

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Basic information

Entry
Database: PDB / ID: 1b9l
Title7,8-DIHYDRONEOPTERIN TRIPHOSPHATE EPIMERASE
ComponentsPROTEIN (EPIMERASE)
KeywordsISOMERASE / EPIMERASE
Function / homology
Function and homology information


dihydroneopterin triphosphate 2'-epimerase / dihydroneopterin triphosphate 2'-epimerase activity / dihydroneopterin aldolase activity / folic acid-containing compound metabolic process / cytosol / cytoplasm
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
Dihydroneopterin triphosphate 2'-epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.9 Å
AuthorsPloom, T. / Haussmann, C. / Hof, P. / Steinbacher, S. / Bacher, A. / Richardson, J. / Huber, R.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of 7,8-dihydroneopterin triphosphate epimerase.
Authors: Ploom, T. / Haussmann, C. / Hof, P. / Steinbacher, S. / Bacher, A. / Richardson, J. / Huber, R.
History
DepositionFeb 11, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (EPIMERASE)
B: PROTEIN (EPIMERASE)
C: PROTEIN (EPIMERASE)
D: PROTEIN (EPIMERASE)
E: PROTEIN (EPIMERASE)
F: PROTEIN (EPIMERASE)
G: PROTEIN (EPIMERASE)
H: PROTEIN (EPIMERASE)


Theoretical massNumber of molelcules
Total (without water)112,8248
Polymers112,8248
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: PROTEIN (EPIMERASE)
B: PROTEIN (EPIMERASE)
C: PROTEIN (EPIMERASE)
D: PROTEIN (EPIMERASE)


Theoretical massNumber of molelcules
Total (without water)56,4124
Polymers56,4124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-10 kcal/mol
Surface area22670 Å2
MethodPISA
3
E: PROTEIN (EPIMERASE)
F: PROTEIN (EPIMERASE)
G: PROTEIN (EPIMERASE)
H: PROTEIN (EPIMERASE)


Theoretical massNumber of molelcules
Total (without water)56,4124
Polymers56,4124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-11 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.680, 69.680, 239.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.065617, -0.94851, 0.309876), (-0.950524, -0.153913, -0.269841), (0.303641, -0.276838, -0.911681)35.25, 42.81, 9.65
2given(0.906619, 0.155859, 0.39211), (0.156764, -0.987182, 0.02993), (0.391749, 0.034334, -0.919431)-5.55, 71.73, -1.81
3given(-0.993058, -0.115759, 0.020893), (-0.11762, 0.974983, -0.18861), (0.001462, -0.189758, -0.98183)6.44, 0.93, 6.83
4given(-0.171395, 0.9791, 0.109482), (0.981661, 0.160307, 0.10317), (0.083463, 0.125157, -0.98862)-34.15, 29.29, -4.6
5given(-0.913386, -0.047477, -0.404317), (-0.019548, -0.986915, 0.16005), (-0.406626, 0.154091, 0.900506)3.74, 71.95, -5.1
6given(0.034214, -0.99222, -0.119702), (0.95782, -0.00164, 0.287364), (-0.285325, -0.124484, 0.950312)36.78, 34.98, 4.93
7given(0.037398, 0.957879, -0.284726), (-0.992334, 0.002012, -0.123569), (-0.117791, 0.287164, 0.950611)-33.6, 37.16, -10.22

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Components

#1: Protein
PROTEIN (EPIMERASE)


Mass: 14103.024 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AC19

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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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
Conc.: 35 % / Common name: ethylene glycol

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceWavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 23361 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 2.93 % / Rmerge(I) obs: 0.119 / Rsym value: 11.9
Reflection
*PLUS
Num. measured all: 68471

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Processing

SoftwareName: X-PLOR / Version: 3.8 / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.259 --RANDOM
Rwork0.188 ---
obs-23361 94.6 %-
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7872 0 0 0 7872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.055
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Version: 3.8 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 23272
Solvent computation
*PLUS
Displacement parameters
*PLUS

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