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- PDB-3cq6: Histidinol-phosphate aminotransferase from Corynebacterium glutam... -

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Basic information

Entry
Database: PDB / ID: 3cq6
TitleHistidinol-phosphate aminotransferase from Corynebacterium glutamicum holo-form (PLP covalently bound )
ComponentsHistidinol-phosphate aminotransferase
KeywordsTRANSFERASE / histidinol-phosphate aminotransferase / Corynebacterium glutamicum / PLP / 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
PHOSPHATE ION / Histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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_conn / 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_conn.pdbx_leaving_atom_flag / _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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidinol-phosphate aminotransferase
C: Histidinol-phosphate aminotransferase
E: Histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,06710
Polymers121,4023
Non-polymers6657
Water6,503361
1
A: Histidinol-phosphate aminotransferase
C: Histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5058
Polymers80,9352
Non-polymers5706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-82 kcal/mol
Surface area25440 Å2
MethodPISA
2
E: Histidinol-phosphate aminotransferase
hetero molecules

E: Histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1254
Polymers80,9352
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7860 Å2
ΔGint-53.7 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.798, 80.017, 88.484
Angle α, β, γ (deg.)90.00, 94.79, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-428-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12C
22E

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEUAA31 - 36634 - 369
21ARGARGLEULEUCB31 - 36634 - 369
31ARGARGLEULEUEC31 - 36634 - 369
12LYSLYSILEILECB3 - 306 - 33
22LYSLYSILEILEEC3 - 306 - 33

NCS ensembles :
ID
1
2

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Components

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


Mass: 40467.496 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: HisC / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9KJU4, histidinol-phosphate transaminase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.4M NaH2PO4, 1.6M K2HPO4, 0.2M NaCl, 0.1M imidazole, 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: ID23-1 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2006
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.1→88 Å / Num. all: 75438 / Num. obs: 75438 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.8 / Num. unique all: 10992 / Rsym value: 0.45 / % possible all: 96.8

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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 3CQ5

3cq5


Resolution: 2.1→30.79 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.508 / SU ML: 0.143 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.211 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23837 3751 5 %RANDOM
Rwork0.19767 ---
all0.19962 71661 --
obs0.19962 71661 96.68 %-
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: 24.872 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å2-0.49 Å2
2--1.55 Å20 Å2
3----3.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8442 0 35 361 8838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228641
X-RAY DIFFRACTIONr_bond_other_d0.0010.025655
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.97711799
X-RAY DIFFRACTIONr_angle_other_deg0.903313788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63251089
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81623.969393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.525151347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1221566
X-RAY DIFFRACTIONr_chiral_restr0.0670.21365
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021725
X-RAY DIFFRACTIONr_nbd_refined0.210.21805
X-RAY DIFFRACTIONr_nbd_other0.1960.26205
X-RAY DIFFRACTIONr_nbtor_refined0.1750.24319
X-RAY DIFFRACTIONr_nbtor_other0.0860.24457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2393
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.212
X-RAY DIFFRACTIONr_mcbond_it0.7381.56963
X-RAY DIFFRACTIONr_mcbond_other0.1461.52187
X-RAY DIFFRACTIONr_mcangle_it0.85428802
X-RAY DIFFRACTIONr_scbond_it1.53633639
X-RAY DIFFRACTIONr_scangle_it2.3024.52997
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1978medium positional0.170.5
12C1978medium positional0.170.5
13E1978medium positional0.10.5
21C163medium positional0.090.5
11A2358loose positional0.375
12C2358loose positional0.35
13E2358loose positional0.255
21C200loose positional0.225
11A1978medium thermal0.582
12C1978medium thermal0.742
13E1978medium thermal1.072
21C163medium thermal0.652
11A2358loose thermal1.0710
12C2358loose thermal1.110
13E2358loose thermal1.5310
21C200loose thermal1.0210
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 306 -
Rwork0.288 5253 -
obs-5253 96.64 %

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