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- PDB-1uu1: Complex of Histidinol-phosphate aminotransferase (HisC) from Ther... -

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Basic information

Entry
Database: PDB / ID: 1uu1
TitleComplex of Histidinol-phosphate aminotransferase (HisC) from Thermotoga maritima (Apo-form)
ComponentsHISTIDINOL-PHOSPHATE AMINOTRANSFERASE
KeywordsTRANSFERASE / HISTIDINE BIOSYNTHESIS / AMINOTRANSFERASE / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


histidinol-phosphate transaminase / histidinol-phosphate transaminase activity / L-histidine biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity
Similarity search - Function
: / Histidinol-phosphate aminotransferase family / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...: / Histidinol-phosphate aminotransferase family / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HSA / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsVega, M.C. / Fernandez, F.J. / Lehman, F. / Wilmanns, M.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Structural Studies of the Catalytic Reaction Pathway of a Hyperthermophilic Histidinol-Phosphate Aminotransferase
Authors: Fernandez, F.J. / Vega, M.C. / Lehmann, F. / Sandmeier, E. / Gehring, H. / Christen, P. / Wilmanns, M.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of Histidinol Phosphate Aminotransferase (Hisc) from Escherichia Coli, and its Covalent Complex with Pyridoxal-5'-Phosphate and L-Histidinol Phosphate
Authors: Sivaraman, J. / Li, Y. / Larocque, R. / Schrag, J.D. / Cygler, M. / Matte, A.
History
DepositionDec 12, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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

Downloads & links

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Assembly

Deposited unit
A: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
B: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
C: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
D: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,28112
Polymers157,4044
Non-polymers1,8778
Water6,648369
1
A: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
B: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6416
Polymers78,7022
Non-polymers9394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
D: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6416
Polymers78,7022
Non-polymers9394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.610, 136.519, 92.815
Angle α, β, γ (deg.)90.00, 95.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HISTIDINOL-PHOSPHATE AMINOTRANSFERASE / IMIDAZOLE ACETOL-PHOSPHATE TRANAMINASE / HISC


Mass: 39350.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: PHOSPHATE ANION ATTACHED PER CHAIN / Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9X0D0, histidinol-phosphate transaminase
#2: Chemical
ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Chemical
ChemComp-HSA / PHOSPHORIC ACID MONO-[2-AMINO-3-(3H-IMIDAZOL-4-YL)-PROPYL]ESTER


Mass: 221.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12N3O4P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 44.7 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMHEPES1droppH7.5
210 mMdithiothreitol1drop
32 mMEDTA1drop
435 mg/mlprotein1drop
550 %(v/v)ethylene glycol1reservoir
65 %(w/v)PEG10001reservoirpH5.1
7sodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8042
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8042 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. obs: 49556 / % possible obs: 90.6 % / Redundancy: 1.25 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.0885 / Net I/σ(I): 12.7
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 1 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.22 / % possible all: 91.3
Reflection
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 20 Å / Redundancy: 2.3 % / Num. measured all: 120299 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 91.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H1C

1h1c


Resolution: 2.38→19.67 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2427 5 %RANDOM
Rwork0.206 ---
obs0.206 48181 90.7 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.36114 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.03 Å20 Å20.05 Å2
2--1.76 Å20 Å2
3----8.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.38→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11031 0 116 369 11516
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.38→2.53 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 400 5 %
Rwork0.256 7614 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4HSP.PARHSP.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 49260 / % reflection Rfree: 4.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.478
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

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