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- PDB-1h1c: Histidinol-phosphate aminotransferase (HisC) from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1h1c
TitleHistidinol-phosphate aminotransferase (HisC) from Thermotoga maritima
ComponentsHISTIDINOL-PHOSPHATE AMINOTRANSFERASE
KeywordsTRANSFERASE / AMINOTRANSFERASE / HISTIDINE BIOSYNTHESIS
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
PYRIDOXAL-5'-PHOSPHATE / Histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsVega, M.C. / Fernandez, F.J. / 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
DepositionJul 8, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2004Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)160,0818
Polymers159,0924
Non-polymers9894
Water2,396133
1
A: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
B: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0404
Polymers79,5462
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-31 kcal/mol
Surface area26070 Å2
MethodPISA
2
C: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
D: HISTIDINOL-PHOSPHATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0404
Polymers79,5462
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-29.3 kcal/mol
Surface area26250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.666, 146.168, 54.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.84674, 0.30864, 0.43333), (0.35322, -0.28294, 0.89173), (0.39783, 0.90812, 0.13056)14.92868, 53.65038, -48.14807
2given(0.46921, 0.51663, 0.71619), (0.00198, 0.81039, -0.58588), (-0.88308, 0.27632, 0.37922)-56.19446, -5.72235, 11.63761
3given(0.04461, 0.65203, 0.75688), (0.03422, -0.75818, 0.65114), (0.99842, -0.00314, -0.05613)-55.67696, 66.12294, -5.12314

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Components

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


Mass: 39772.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: RESIDUE 202 LYSINE-PYRIDOXAL-5'-PHOSPHATE / Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q9X0D0, histidinol-phosphate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONVERTS L-HISTIDINOL-PHOSPHATE + 2-OXOGLUTARATE TO 3- (IMIDAZOL-4-YL)-2-OXOPROPYL PHOSPHATE + L- ...CONVERTS L-HISTIDINOL-PHOSPHATE + 2-OXOGLUTARATE TO 3- (IMIDAZOL-4-YL)-2-OXOPROPYL PHOSPHATE + L-GLUTAMATE. MEMBER OF THE CLASS-II OF PYRIDOXAL-PHOSPHATE-DEPENDENT AMINOTRANSFERASES.

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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: 2.53 Å3/Da / Density % sol: 51 %
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
540 %(v/v)ethylene glycol1reservoir
60.1 Msodium acetate1reservoirpH6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9778,0.9862,0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97781
20.98621
30.91841
ReflectionResolution: 2.85→20 Å / Num. obs: 29624 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 6.98
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.38 / % possible all: 95.7
Reflection
*PLUS
Highest resolution: 2.85 Å / Lowest resolution: 20 Å

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.85→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3206 10 %RANDOM
Rwork0.258 ---
obs0.258 33722 93.4 %-
Displacement parametersBiso mean: 21.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---1.21 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10615 0 60 133 10808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg0.944
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.85→2.914 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 155
Rwork0.349 1398
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 9.3 % / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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