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- PDB-2rkx: The 3D structure of chain D, cyclase subunit of imidazoleglycerol... -

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Basic information

Entry
Database: PDB / ID: 2rkx
TitleThe 3D structure of chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase
ComponentsCyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase
KeywordsLYASE / Alpha-Beta Barrel / Structural Genomics / Israel Structural Proteomics Center / ISPC / Amino-acid biosynthesis / Cytoplasm / Histidine biosynthesis
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsTawfik, D. / Khersonsky, O. / Albeck, S. / Dym, O. / Israel Structural Proteomics Center (ISPC)
CitationJournal: Nature / Year: 2008
Title: Kemp elimination catalysts by computational enzyme design.
Authors: Rothlisberger, D. / Khersonsky, O. / Wollacott, A.M. / Jiang, L. / DeChancie, J. / Betker, J. / Gallaher, J.L. / Althoff, E.A. / Zanghellini, A. / Dym, O. / Albeck, S. / Houk, K.N. / Tawfik, D.S. / Baker, D.
History
DepositionOct 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase


Theoretical massNumber of molelcules
Total (without water)28,0511
Polymers28,0511
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.380, 96.380, 153.988
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase


Mass: 28051.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic protein / References: Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS PROVIDED TARGETDB ID W00826 WHICH DOES NOT EXIST IN THE TARGET DATABASE.

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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: 3.71 Å3/Da / Density % sol: 66.88 %
Crystal growTemperature: 292 K / Method: microbatch under oil / pH: 7
Details: 20% PEG 3350, 0.1M Bis-Tris propane pH 8.5, 0.2M NaF, pH 7.0, MICROBATCH UNDER OIL, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 18, 2007 / Details: Mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 20784 / Num. obs: 20784 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 19.7 % / Rmerge(I) obs: 0.098 / Rsym value: 0.087 / Net I/σ(I): 36.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 18.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 6.8 / Num. unique all: 2025 / Rsym value: 0.392 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1THF

1thf


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.623 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23481 1066 5.1 %RANDOM
Rwork0.2057 ---
obs0.20716 19657 99.55 %-
all-19746 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.665 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 0 102 2042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221971
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9622657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46723.83786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8115357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2641514
X-RAY DIFFRACTIONr_chiral_restr0.1160.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021455
X-RAY DIFFRACTIONr_nbd_refined0.2070.2855
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21348
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2111
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.211
X-RAY DIFFRACTIONr_mcbond_it1.291.51288
X-RAY DIFFRACTIONr_mcangle_it2.01621978
X-RAY DIFFRACTIONr_scbond_it3.343788
X-RAY DIFFRACTIONr_scangle_it5.0384.5679
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 65 -
Rwork0.239 1358 -
obs--95.38 %

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