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- PDB-3cq5: Histidinol-phosphate aminotransferase from Corynebacterium glutam... -

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Basic information

Entry
Database: PDB / ID: 3cq5
TitleHistidinol-phosphate aminotransferase from Corynebacterium glutamicum in complex with PMP
ComponentsHistidinol-phosphate aminotransferase
KeywordsTRANSFERASE / histidinol-phosphate aminotransferase / Corynebacterium glutamicum / PLP / PMP / 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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.2Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,40515
Polymers120,7183
Non-polymers1,68712
Water13,980776
1
A: Histidinol-phosphate aminotransferase
B: Histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,60410
Polymers80,4792
Non-polymers1,1258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-104.1 kcal/mol
Surface area25270 Å2
MethodPISA
2
C: Histidinol-phosphate aminotransferase
hetero molecules

C: Histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,60410
Polymers80,4792
Non-polymers1,1258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10070 Å2
ΔGint-100.4 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.273, 85.531, 89.431
Angle α, β, γ (deg.)90.00, 93.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-522-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SO4 / End label comp-ID: SO4 / Refine code: 5 / Auth seq-ID: 3 - 402 / Label seq-ID: 6

Dom-IDAuth asym-IDLabel asym-ID
1AA - D
2BB - J
3CC - L

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Components

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


Mass: 40239.375 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3
#4: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H13N2O5P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 776 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.7M (NH4)2SO4, 0.2M Li2SO4, 0.1M Tris, pH 7.0, 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: 1.8→78 Å / Num. all: 133625 / Num. obs: 133625 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.7 / Num. unique all: 19316 / Rsym value: 0.456 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.486 / SU ML: 0.078 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.114 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21916 6716 5 %RANDOM
Rwork0.19179 ---
all0.19313 126870 --
obs0.19313 126870 98.25 %-
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: 21.233 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å2-0.09 Å2
2--0.45 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8424 0 102 776 9302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228683
X-RAY DIFFRACTIONr_bond_other_d0.0020.025689
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.98111852
X-RAY DIFFRACTIONr_angle_other_deg0.9253.00113825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.41951090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7323.969393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.305151351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8021566
X-RAY DIFFRACTIONr_chiral_restr0.1270.21372
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021726
X-RAY DIFFRACTIONr_nbd_refined0.220.21928
X-RAY DIFFRACTIONr_nbd_other0.2010.26487
X-RAY DIFFRACTIONr_nbtor_refined0.1770.24406
X-RAY DIFFRACTIONr_nbtor_other0.0870.24450
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2642
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1360.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.080.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.235
X-RAY DIFFRACTIONr_mcbond_it0.8491.56991
X-RAY DIFFRACTIONr_mcbond_other0.321.52189
X-RAY DIFFRACTIONr_mcangle_it0.99128819
X-RAY DIFFRACTIONr_scbond_it2.07733657
X-RAY DIFFRACTIONr_scangle_it2.7684.53033
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2137medium positional0.120.5
2B2137medium positional0.140.5
3C2137medium positional0.110.5
1A2578loose positional0.45
2B2578loose positional0.365
3C2578loose positional0.315
1A2137medium thermal2.152
2B2137medium thermal1.352
3C2137medium thermal2.572
1A2578loose thermal2.5610
2B2578loose thermal1.8910
3C2578loose thermal3.0610
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 532 -
Rwork0.264 9202 -
obs-9202 97.43 %

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