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- PDB-3g0t: Crystal structure of putative aspartate aminotransferase (NP_9054... -

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Basic information

Entry
Database: PDB / ID: 3g0t
TitleCrystal structure of putative aspartate aminotransferase (NP_905498.1) from Porphyromonas gingivalis W83 at 1.75 A resolution
ComponentsPutative aminotransferaseTransaminase
KeywordsTRANSFERASE / NP_905498.1 / putative aspartate aminotransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Aminotransferase
Function / homology
Function and homology information


transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #100 / 434 Repressor (Amino-terminal Domain) / Bacterial aspartate aminotransferase, helical domain / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Helix non-globular / Pyridoxal phosphate-dependent transferase, major domain ...Aspartate Aminotransferase, domain 1 - #100 / 434 Repressor (Amino-terminal Domain) / Bacterial aspartate aminotransferase, helical domain / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Helix non-globular / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Special / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aminotransferase, putative
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Protein Sci. / Year: 2014
Title: Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome.
Authors: Fleischman, N.M. / Das, D. / Kumar, A. / Xu, Q. / Chiu, H.J. / Jaroszewski, L. / Knuth, M.W. / Klock, H.E. / Miller, M.D. / Elsliger, M.A. / Godzik, A. / Lesley, S.A. / Deacon, A.M. / Wilson, I.A. / Toney, M.D.
History
DepositionJan 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.4Jul 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 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_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

Downloads & links

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Assembly

Deposited unit
A: Putative aminotransferase
B: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,77127
Polymers100,7662
Non-polymers2,00525
Water20,3031127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-17.5 kcal/mol
Surface area30130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.440, 54.970, 81.154
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative aminotransferase / Transaminase


Mass: 50382.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: NP_905498.1, PG_1327 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q7MUZ3

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Non-polymers , 5 types, 1152 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1127 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: NANODROP, 0.20M NaF, 20.0% PEG 3350, No Buffer pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645, 0.97967
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979671
ReflectionResolution: 1.75→34.401 Å / Num. obs: 96949 / % possible obs: 96.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 5.515
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.81.90.3961.7994053240.39673.9
1.8-1.843.70.471.52214160050.4784.4
1.84-1.94.30.3781.92838466420.37895.9
1.9-1.965.30.3052.43545066700.30598.9
1.96-2.026.30.2612.84117165290.26199.9
2.02-2.096.70.2083.54241963760.20899.9
2.09-2.176.90.1844211361120.18100
2.17-2.267.20.1544.64281859330.154100
2.26-2.367.70.1444.84344556630.144100
2.36-2.477.70.1235.64207754860.123100
2.47-2.617.70.1096.33982451900.109100
2.61-2.777.70.0966.93788249260.096100
2.77-2.967.70.0926.93581546350.092100
2.96-3.27.70.0847.33341143190.084100
3.2-3.57.70.0787.63123740400.078100
3.5-3.917.70.07382798536360.073100
3.91-4.527.70.0619.92469432240.061100
4.52-5.537.50.0648.72088127670.064100
5.53-7.837.40.05810.91623221920.058100
7.83-34.4016.80.0686.8872612800.06898.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→34.401 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 4.162 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.094
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. NA AND CL IONS FROM THE PURIFICATION MEDIA ARE MODELED. 5. ETHYLENE GLYCOL MOLECULES FROM THE CRYO SOLUTION ARE MODELED. 6. FRAGMENTS OF PEG 3350 (PE4) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 7. RESIDUE LYS 259 IS MODELED AS LLP BECAUSE OF ITS COVALENT LINKAGE TO A PYRIDOXAL-5'-PHOSPHATE (PLP) MOLECULE BOUND TO THE PROTEIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.171 4788 5 %RANDOM
Rwork0.137 ---
obs0.139 96109 95.59 %-
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 max: 60.89 Å2 / Biso mean: 16.524 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.53 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→34.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 0 97 1127 8126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227425
X-RAY DIFFRACTIONr_bond_other_d0.0010.025274
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.98410023
X-RAY DIFFRACTIONr_angle_other_deg0.971312827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5635954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07323.904356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.293151335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4061557
X-RAY DIFFRACTIONr_chiral_restr0.1090.21065
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218295
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021550
X-RAY DIFFRACTIONr_mcbond_it1.1924464
X-RAY DIFFRACTIONr_mcbond_other0.28521822
X-RAY DIFFRACTIONr_mcangle_it2.00847209
X-RAY DIFFRACTIONr_scbond_it3.49162961
X-RAY DIFFRACTIONr_scangle_it4.96382773
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 247 -
Rwork0.229 4961 -
all-5208 -
obs--71.4 %
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)
10.2859-0.14220.20820.4075-0.1790.5241-0.03890.0427-0.01270.01790.03830.00080.02450.03050.00050.0272-0.0142-0.00520.0266-0.00770.061742.41113.11168.912
20.4214-0.08160.28220.2842-0.06560.68060.0783-0.0525-0.0105-0.0315-0.05070.01350.0465-0.0178-0.02750.055-0.0296-0.00110.0346-0.00570.071617.5212.22642.222
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 436
2X-RAY DIFFRACTION2B2 - 436

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