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- PDB-1h5y: HisF protein from Pyrobaculum aerophilum -

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Basic information

Entry
Database: PDB / ID: 1h5y
TitleHisF protein from Pyrobaculum aerophilum
ComponentsHISF
KeywordsHISTIDINE BIOSYNTHESIS / TIM-BARREL
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / L-histidine biosynthetic process / lyase activity / cytoplasm
Similarity search - Function
Histidine biosynthesis, HisF / : / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Imidazole glycerol phosphate synthase subunit HisF
Similarity search - Component
Biological speciesPYROBACULUM AEROPHILUM (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBanfield, M.J. / Lott, J.S. / McCarthy, A.A. / Baker, E.N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Hisf, a Histidine Biosynthetic Protein from Pyrobaculum Aerophilum
Authors: Banfield, M.J. / Lott, J.S. / Arcus, V. / Mccarthy, A.A. / Baker, E.N.
#1: Journal: Science / Year: 2000
Title: Structural Evidence for Evolution of the Beta/Alpha Barrel Scaffold by Gene Duplication and Fusion
Authors: Lang, D. / Thoma, R. / Henn-Sax, M. / Sterner, R. / Wilmanns, M.
History
DepositionMay 31, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" ON SHEET RECORDS BELOW IS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISF
B: HISF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,77010
Polymers54,0212
Non-polymers7488
Water4,846269
1
A: HISF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3855
Polymers27,0111
Non-polymers3744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HISF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3855
Polymers27,0111
Non-polymers3744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.896, 105.896, 141.828
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.054498, 0.998325, -0.019398), (0.997412, -0.053516, 0.048006), (0.046888, -0.021964, -0.998659)
Vector: 46.547, -12.807, -10.882)

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Components

#1: Protein HISF


Mass: 27010.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RESIDUES 1-3 OF THE INTACT SEQUENCE ARE NOT PRESENT IN THE EXPRESSED PROTEIN
Source: (gene. exp.) PYROBACULUM AEROPHILUM (archaea) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21 / References: UniProt: Q8ZY16*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN IDENTIFIED AS AN OPEN READING FRAME FROM THE P. AEROPHILUM GENOME.

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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: 4.26 Å3/Da / Density % sol: 65.5 %
Crystal growpH: 5.6
Details: 10MG/ML PROTEIN IN 50MM TRIS PH 7.5, 150MM NACL. 100MM SODIUM CITRATE (PH5.6), 0.9-1.0M AMMONIUM PHOSPHATE.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein11
2100 mMsodium citrate12pH5.6
30.9-1.0 Mammonium dihydrogen phosphate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 59658 / % possible obs: 98.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.1
Reflection shellResolution: 2→2.09 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.7 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 25 Å
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1THF

1thf


Resolution: 2→25 Å / SU B: 3.25009 / SU ML: 0.09364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.12492
Details: N-TERMINAL RESIDUES HIS-A2, MET-A3, SER-B1, HIS-B2, MET-3 ARE CLONING ARTEFACTS DERIVED FROM THE HIS-TAG, BUT ARE OBSERVED IN THE ELECTRON DENSITY. THE EXPRESSED PROTEIN COMPRISED RESIDUES ...Details: N-TERMINAL RESIDUES HIS-A2, MET-A3, SER-B1, HIS-B2, MET-3 ARE CLONING ARTEFACTS DERIVED FROM THE HIS-TAG, BUT ARE OBSERVED IN THE ELECTRON DENSITY. THE EXPRESSED PROTEIN COMPRISED RESIDUES ALA-4 - ILE-253 OF THE NATIVE HISF SEQUENCE. THE FOLLOWING RESIDUES HAVE BEEN MODELLED IN ALTERNATE CONFORMATIONS: ARG-A30, ARG-A121, ASP- A222 ARG-B30, ASP-222 RESIDUES ARG-B111 AND ARG-B121 HAVE NO INTERPRETABLE SIDE-CHAIN ELECTRON DENSITY FOR THE FOLLWOING ATOMS, WHICH HAVE BEEN SET TO ZERO OCCUPANCY: ARG-B111: CG, CD, NE, CZ, NH1, NH2 ARG-B121: CD, NE, CZ, NH1, NH2
RfactorNum. reflection% reflectionSelection details
Rfree0.22724 3021 5.1 %RANDOM
Rwork0.20565 ---
obs0.20675 56594 98.3 %-
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3745 0 44 269 4058
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.09 Å / Rfactor Rfree: 0.29 / Rfactor obs: 0.24

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