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- PDB-3cq4: Histidinol-phosphate aminotransferase from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 3cq4
TitleHistidinol-phosphate aminotransferase from Corynebacterium glutamicum
ComponentsHistidinol-phosphate aminotransferase
KeywordsTRANSFERASE / histidinol-phosphate aminotransferase / Corynebacterium glutamicum / PLP / strep-tag / Amino-acid biosynthesis / Histidine biosynthesis / Pyridoxal phosphate
Function / homology
Function and homology information


histidinol-phosphate transaminase / histidinol-phosphate transaminase activity / L-histidine biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Histidinol-phosphate aminotransferase family / 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 ...Histidinol-phosphate aminotransferase family / 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
ACETATE ION / Histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSandalova, T. / Marienhagen, J. / Schneider, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Insights into the structural basis of substrate recognition by histidinol-phosphate aminotransferase from Corynebacterium glutamicum
Authors: Marienhagen, J. / Sandalova, T. / Sahm, H. / Eggeling, L. / Schneider, G.
History
DepositionApr 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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: Histidinol-phosphate aminotransferase
B: Histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4334
Polymers82,3152
Non-polymers1182
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-36.6 kcal/mol
Surface area28650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.340, 102.340, 140.108
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 5 - 355 / Label seq-ID: 5 - 355

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Histidinol-phosphate aminotransferase / Imidazole acetol-phosphate transaminase


Mass: 41157.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: HisC / Plasmid: pASK-IBA-3C / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 MCR
References: UniProt: Q9KJU4, histidinol-phosphate transaminase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 9% PEG 6K, 1M lithium acetate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 11, 2006
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→54.9 Å / Num. all: 43528 / Num. obs: 43528 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 25.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.7 / Num. unique all: 6295 / Rsym value: 0.53 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UU1

1uu1


Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.272 / SU ML: 0.185 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.292 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27674 2175 5 %RANDOM
Rwork0.23708 ---
all0.23908 41180 --
obs0.23908 41180 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.646 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5411 0 8 217 5636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225519
X-RAY DIFFRACTIONr_bond_other_d0.0020.023634
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9667517
X-RAY DIFFRACTIONr_angle_other_deg1.0138863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1545696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61523.968247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60315876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8311541
X-RAY DIFFRACTIONr_chiral_restr0.0780.2888
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026168
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021103
X-RAY DIFFRACTIONr_nbd_refined0.2050.21225
X-RAY DIFFRACTIONr_nbd_other0.1980.23855
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22728
X-RAY DIFFRACTIONr_nbtor_other0.0870.22835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.28
X-RAY DIFFRACTIONr_mcbond_it0.8631.54476
X-RAY DIFFRACTIONr_mcbond_other0.1471.51409
X-RAY DIFFRACTIONr_mcangle_it0.99525665
X-RAY DIFFRACTIONr_scbond_it1.38832277
X-RAY DIFFRACTIONr_scangle_it2.0824.51852
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1948tight positional0.070.05
2298medium positional0.40.5
1948tight thermal0.130.5
2298medium thermal0.512
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 139 -
Rwork0.357 2915 -
obs--95.32 %

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