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- PDB-3ezs: Crystal structure of aminotransferase AspB (NP_207418.1) from HEL... -

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Basic information

Entry
Database: PDB / ID: 3ezs
TitleCrystal structure of aminotransferase AspB (NP_207418.1) from HELICOBACTER PYLORI 26695 at 2.19 A resolution
Componentsaminotransferase AspB
KeywordsTRANSFERASE / NP_207418.1 / aminotransferase AspB / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Aminotransferase class I and II
Function / homology
Function and homology information


biosynthetic process / catalytic activity / 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 / Solute-binding signature and mitochondrial signature protein (AspB)
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.19 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of aminotransferase AspB (NP_207418.1) from HELICOBACTER PYLORI 26695 at 2.19 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 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: aminotransferase AspB
B: aminotransferase AspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,43512
Polymers86,7482
Non-polymers68610
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-33 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.648, 106.249, 80.201
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 5 / Auth seq-ID: 0 - 373 / Label seq-ID: 0 - 373

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

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Components

#1: Protein aminotransferase AspB / Solute-binding signature and mitochondrial signature protein (AspB)


Mass: 43374.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: NP_207418.1, HP_0624 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: O25341
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15.0000% Glycerol, 8.5000% iso-Propanol, 17.0000% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 11, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979321
ReflectionResolution: 2.19→44.281 Å / Num. obs: 40833 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 29.514 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.19-2.270.6122.29128713568185.8
2.27-2.360.553.22227740391100
2.36-2.470.44742310741931100
2.47-2.60.3624.92247140701100
2.6-2.760.2636.52227640421100
2.76-2.970.1938.72249240831100
2.97-3.270.12612.82275041481100
3.27-3.740.07620.22260941521100
3.74-4.70.04529.8226594193199.7
4.7-44.2810.04132.4230104373198.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.19→44.281 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 10.513 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.198
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN 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 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. ETHYLENE GLYCOL (EDO) USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE. 5. BASED ON HOMOLOGUS STRUCTURES THAT BIND PYRIDOXAL-5'PHOSPHATE (PLP), SUCH AS 1O4S, A PHOSPHATE MOLECULE HAS BEEN MODELED IN EACH CHAIN AT THE SITE OF THE CORRESPONDING PHOSPHATE MOIETY OF PLP. THERE IS NO ELECTRON DENSITY SUPPORT FOR THE REST OF THE PLP MOLECULE
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2056 5 %RANDOM
Rwork0.159 ---
obs0.161 40803 98.46 %-
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: 84.51 Å2 / Biso mean: 43.55 Å2 / Biso min: 19.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.19→44.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5988 0 42 402 6432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226285
X-RAY DIFFRACTIONr_bond_other_d0.0020.024361
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9828539
X-RAY DIFFRACTIONr_angle_other_deg1.012310628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4455780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37623.759290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.377151064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2111538
X-RAY DIFFRACTIONr_chiral_restr0.0880.2938
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021320
X-RAY DIFFRACTIONr_nbd_refined0.2010.31249
X-RAY DIFFRACTIONr_nbd_other0.1760.34339
X-RAY DIFFRACTIONr_nbtor_refined0.180.53042
X-RAY DIFFRACTIONr_nbtor_other0.0860.52933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.5533
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.521
X-RAY DIFFRACTIONr_mcbond_it1.49833987
X-RAY DIFFRACTIONr_mcbond_other0.43231500
X-RAY DIFFRACTIONr_mcangle_it2.27456160
X-RAY DIFFRACTIONr_scbond_it4.29182705
X-RAY DIFFRACTIONr_scangle_it5.549112364
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
2180MEDIUM POSITIONAL0.230.5
2768LOOSE POSITIONAL0.435
2180MEDIUM THERMAL0.742
2768LOOSE THERMAL1.8310
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 115 -
Rwork0.215 2341 -
all-2456 -
obs--81.62 %
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)
10.56620.0352-0.10210.9599-0.14230.7521-0.0177-0.02520.0053-0.02050.0125-0.07360.02330.02230.0053-0.09960.0093-0.0251-0.1148-0.0081-0.090426.38725.05637.248
20.6566-0.13310.04750.7101-0.03161.2137-0.0410.0167-0.0481-0.025-0.01310.0401-0.00630.00430.0541-0.1181-0.0056-0.0045-0.0827-0.0132-0.109536.08520.1771.932
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 373
2X-RAY DIFFRACTION2B0 - 373

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