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- PDB-4evz: Structure of HisF-LUCA -

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Basic information

Entry
Database: PDB / ID: 4evz
TitleStructure of HisF-LUCA
ComponentsHisF-LUCA
KeywordsLYASE / Imidazole glycerol phosphate synthase-LUCA
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / HYDROGENPHOSPHATE ION
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.462 Å
AuthorsReisinger, B. / Sperl, J. / Rajendran, C. / Merkl, R. / Sterner, R.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Evidence for the existence of elaborate enzyme complexes in the Paleoarchean era.
Authors: Reisinger, B. / Sperl, J. / Holinski, A. / Schmid, V. / Rajendran, C. / Carstensen, L. / Schlee, S. / Blanquart, S. / Merkl, R. / Sterner, R.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: HisF-LUCA
B: HisF-LUCA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2236
Polymers55,8392
Non-polymers3844
Water12,016667
1
A: HisF-LUCA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1113
Polymers27,9191
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HisF-LUCA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1113
Polymers27,9191
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.074, 90.736, 57.369
Angle α, β, γ (deg.)90.00, 100.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HisF-LUCA / Imidazole glycerol phosphate synthase / resurrected


Mass: 27919.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) artificial gene (others)
#2: Chemical
ChemComp-PI / HYDROGENPHOSPHATE ION


Mass: 95.979 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HO4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→56.454 Å / Num. all: 74891 / Num. obs: 69542 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.12

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
CCP4suitephasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1THF

1thf


Resolution: 1.462→47.934 Å / SU ML: 0.13 / σ(F): 2.07 / Phase error: 16.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1761 3476 5 %RANDOM
Rwork0.1514 ---
obs0.1526 69536 92.85 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.091 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0261 Å2-0 Å20.0285 Å2
2---0.0145 Å20 Å2
3----0.0116 Å2
Refinement stepCycle: LAST / Resolution: 1.462→47.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 20 667 4541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013928
X-RAY DIFFRACTIONf_angle_d1.2945312
X-RAY DIFFRACTIONf_dihedral_angle_d10.9421419
X-RAY DIFFRACTIONf_chiral_restr0.071607
X-RAY DIFFRACTIONf_plane_restr0.006697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.462-1.48180.3208390.2716738X-RAY DIFFRACTION26
1.4818-1.5030.2726960.22691819X-RAY DIFFRACTION64
1.503-1.52540.19891120.17142137X-RAY DIFFRACTION75
1.5254-1.54920.21761260.16762382X-RAY DIFFRACTION84
1.5492-1.57460.23151310.15412501X-RAY DIFFRACTION90
1.5746-1.60180.18571430.15382716X-RAY DIFFRACTION94
1.6018-1.63090.18551460.14772761X-RAY DIFFRACTION99
1.6309-1.66230.19681510.14772868X-RAY DIFFRACTION100
1.6623-1.69620.17471470.14612796X-RAY DIFFRACTION100
1.6962-1.73310.18521510.152867X-RAY DIFFRACTION100
1.7331-1.77340.17051480.14072815X-RAY DIFFRACTION100
1.7734-1.81780.17651490.13952836X-RAY DIFFRACTION100
1.8178-1.86690.17111500.14372845X-RAY DIFFRACTION100
1.8669-1.92190.15991480.13552813X-RAY DIFFRACTION100
1.9219-1.98390.17451490.13872824X-RAY DIFFRACTION99
1.9839-2.05480.15491500.13872859X-RAY DIFFRACTION100
2.0548-2.13710.18351470.13982794X-RAY DIFFRACTION99
2.1371-2.23430.14921490.13472824X-RAY DIFFRACTION99
2.2343-2.35210.16011490.1332826X-RAY DIFFRACTION99
2.3521-2.49950.16991500.14022847X-RAY DIFFRACTION99
2.4995-2.69250.17491480.1512810X-RAY DIFFRACTION99
2.6925-2.96340.16631470.14572818X-RAY DIFFRACTION99
2.9634-3.39210.15291490.1542842X-RAY DIFFRACTION99
3.3921-4.27330.1611490.14842836X-RAY DIFFRACTION99
4.2733-47.95930.20981520.19592886X-RAY DIFFRACTION99

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