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- PDB-3ftb: The crystal structure of the histidinol-phosphate aminotransferas... -

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Basic information

Entry
Database: PDB / ID: 3ftb
TitleThe crystal structure of the histidinol-phosphate aminotransferase from Clostridium acetobutylicum
ComponentsHistidinol-phosphate aminotransferase
KeywordsTRANSFERASE / Histidinol-phosphate aminotransferase / Structural Genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / Aminotransferase
Function / homology
Function and homology information


transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
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 ...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
PHOSPHATE ION / Histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, R. / Bigelow, L. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the histidinol-phosphate aminotransferase from Clostridium acetobutylicum
Authors: Zhang, R. / Bigelow, L. / Moy, S. / Joachimiak, A.
History
DepositionJan 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

Deposited unit
A: Histidinol-phosphate aminotransferase
B: Histidinol-phosphate aminotransferase
D: Histidinol-phosphate aminotransferase
E: Histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,82814
Polymers164,8794
Non-polymers95010
Water10,827601
1
A: Histidinol-phosphate aminotransferase
B: Histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9147
Polymers82,4392
Non-polymers4755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-45 kcal/mol
Surface area26560 Å2
MethodPISA
2
D: Histidinol-phosphate aminotransferase
E: Histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9147
Polymers82,4392
Non-polymers4755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-44 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.556, 121.663, 94.185
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211
Detailsauthors state that this protein existed as dimer.

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Components

#1: Protein
Histidinol-phosphate aminotransferase


Mass: 41219.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Gene: CA_C1369, GI:15894648, hisC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q97JB7
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% Ethanol, 0.1M Tris , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 250K, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→37.25 Å / Num. all: 211748 / Num. obs: 178715 / % possible obs: 89.44 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 25.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.89 / Num. unique all: 14882 / % possible all: 62.45

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CNSrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→37.248 Å / Isotropic thermal model: unisotropic / Cross valid method: THROUGHOUT / σ(F): 1.89 / σ(I): 0 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 9317 5.21 %RANDOM
Rwork0.1745 ---
obs0.1764 178715 89.44 %-
all-211748 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.882 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso mean: 43.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.7277 Å2-0 Å20.4612 Å2
2---14.9804 Å2-0 Å2
3---14.9519 Å2
Refinement stepCycle: LAST / Resolution: 2→37.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10727 0 50 601 11378
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_refined_d0.008
X-RAY DIFFRACTIONf_angle_refined_deg1.008
X-RAY DIFFRACTIONf_chiral_restr0.075
X-RAY DIFFRACTIONf_dihedral_angle_1_deg18.375
X-RAY DIFFRACTIONf_gen_planes_refined0.004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection obs
1.9994-2.03390.32634860.27118808X-RAY DIFFRACTION8808
2.0339-2.07090.27965020.24959071X-RAY DIFFRACTION9071
2.0709-2.11070.29824250.24158835X-RAY DIFFRACTION8835
2.1107-2.15380.27814470.23579087X-RAY DIFFRACTION9087
2.1538-2.20060.24294420.22098966X-RAY DIFFRACTION8966
2.2006-2.25180.45832300.40254427X-RAY DIFFRACTION4427
2.2518-2.30810.39182940.3025781X-RAY DIFFRACTION5781
2.3081-2.37050.23054370.20558874X-RAY DIFFRACTION8874
2.3705-2.44030.22894830.20998844X-RAY DIFFRACTION8844
2.4403-2.5190.24765060.20048802X-RAY DIFFRACTION8802
2.519-2.6090.25324110.20448886X-RAY DIFFRACTION8886
2.609-2.71350.21255220.18618798X-RAY DIFFRACTION8798
2.7135-2.83690.23444750.17898855X-RAY DIFFRACTION8855
2.8369-2.98640.2234620.17838927X-RAY DIFFRACTION8927
2.9864-3.17340.19844610.16469139X-RAY DIFFRACTION9139
3.1734-3.41830.18984930.15599185X-RAY DIFFRACTION9185
3.4183-3.7620.18583960.14217211X-RAY DIFFRACTION7211
3.762-4.30570.15474810.11949018X-RAY DIFFRACTION9018
4.3057-5.4220.15655050.12139018X-RAY DIFFRACTION9018
5.422-37.25460.19145080.15559217X-RAY DIFFRACTION9217
Refinement TLS params.Method: refined / Origin x: 16.5862 Å / Origin y: 13.301 Å / Origin z: 64.7105 Å
111213212223313233
T0.0451 Å2-0.0141 Å20.0015 Å2-0.065 Å20.0114 Å2--0.0809 Å2
L0.103 °2-0.0338 °2-0.0108 °2-0.1606 °20.0452 °2--0.1341 °2
S0.0032 Å °-0.0414 Å °-0.0639 Å °-0.003 Å °-0.0044 Å °0.0274 Å °-0.0125 Å °-0.0036 Å °-0.0031 Å °
Refinement TLS groupSelection details: all

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