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Basic information

Entry
Database: PDB / ID: 3get
TitleCrystal structure of putative histidinol-phosphate aminotransferase (NP_281508.1) from Campylobacter jejuni at 2.01 A resolution
ComponentsHistidinol-phosphate aminotransferase
KeywordsTRANSFERASE / NP_281508.1 / putative histidinol-phosphate aminotransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Amino-acid biosynthesis / Aminotransferase / 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
ISOPROPYL ALCOHOL / Histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni NCTC 11168 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative histidinol-phosphate aminotransferase (NP_281508.1) from Campylobacter jejuni at 2.01 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0905
Polymers83,8782
Non-polymers2123
Water10,160564
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-32.4 kcal/mol
Surface area27790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.745, 79.420, 166.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 12
2113B1 - 12
1212A32 - 364
2212B32 - 364

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Components

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


Mass: 41938.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni NCTC 11168 (Campylobacter)
Strain: NCTC 11168 / Serotype O:2 / Gene: Cj0317, hisC, NP_281508.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q9PII2, histidinol-phosphate transaminase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 10.0% Isopropanol, 20.0% PEG 4000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2008
RadiationMonochromator: Double Crystal Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.01→45.549 Å / Num. obs: 46287 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.545 Å2 / Rmerge(I) obs: 0.085
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.01-2.080.5252100113549175.9
2.08-2.170.4112.6140154743192.3
2.17-2.260.313.6122474056193
2.26-2.380.2783.9148324628195.5
2.38-2.530.215.4160214764198.1
2.53-2.730.1577.1170984909199.4
2.73-30.1099.5169294761199.8
3-3.430.06813.6172264836199.8
3.43-4.320.04417.9169724888199.1
4.32-45.5490.0419.6172825153199

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→45.549 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 10.067 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.185
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RESIDUE LYSINE 226 IN BOTH CHAINS HAS BEEN MODELED AS LLP - A LYSINE WITH A SCHIFF BASE LINKAGE TO PYRIDOXAL-5'PHOSPHATE (PLP). THIS IS THE CONSERVED ACTIVE SITE. 5. 2-PROPANOL AND GLYCEROL MOLECULES FROM CRYSTALLIZATION AND CRYOPROTECTANT WERE MODELED IN THE STRUCTURE, RESPECTIVELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2335 5.1 %RANDOM
Rwork0.174 ---
obs0.177 46226 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 77.6 Å2 / Biso mean: 32.891 Å2 / Biso min: 14.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2---0.37 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.01→45.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5680 0 14 564 6258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225872
X-RAY DIFFRACTIONr_bond_other_d0.0020.023878
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9677943
X-RAY DIFFRACTIONr_angle_other_deg1.08339532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6495739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19225.573262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.842151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3721511
X-RAY DIFFRACTIONr_chiral_restr0.0950.2885
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026581
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021166
X-RAY DIFFRACTIONr_nbd_refined0.2070.31232
X-RAY DIFFRACTIONr_nbd_other0.1670.33985
X-RAY DIFFRACTIONr_nbtor_refined0.1840.52959
X-RAY DIFFRACTIONr_nbtor_other0.090.52807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.5707
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0190.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.335
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.534
X-RAY DIFFRACTIONr_mcbond_it0.8031.53778
X-RAY DIFFRACTIONr_mcbond_other0.231.51485
X-RAY DIFFRACTIONr_mcangle_it1.22525862
X-RAY DIFFRACTIONr_scbond_it2.28932410
X-RAY DIFFRACTIONr_scangle_it3.3654.52081
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
2033TIGHT POSITIONAL0.050.05
2323MEDIUM POSITIONAL0.290.5
81LOOSE POSITIONAL0.365
2033TIGHT THERMAL0.180.5
2323MEDIUM THERMAL0.782
81LOOSE THERMAL0.9610
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 139 -
Rwork0.254 2423 -
all-2562 -
obs--72.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8754-0.2862-0.34021.26740.32351.16580.03170.0454-0.08370.069-0.03380.01810.14180.05380.0021-0.1666-0.0037-0.0027-0.144-0.0115-0.174245.547722.177763.3025
20.2826-0.1925-0.0421.82960.11961.24470.06370.0710.1338-0.1233-0.04450.051-0.1547-0.1341-0.0192-0.16050.01590.0246-0.14060.0262-0.107144.582455.950463.9926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 364
2X-RAY DIFFRACTION2B1 - 364

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