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- PDB-3jtx: Crystal structure of Aminotransferase (NP_283882.1) from NEISSERI... -

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Basic information

Entry
Database: PDB / ID: 3jtx
TitleCrystal structure of Aminotransferase (NP_283882.1) from NEISSERIA MENINGITIDIS Z2491 at 1.91 A resolution
Componentsaminotransferase
KeywordsTRANSFERASE / NP_283882.1 / Aminotransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


succinyldiaminopimelate transaminase activity / lysine biosynthetic process via diaminopimelate / pyridoxal phosphate binding
Similarity search - Function
Succinyldiaminopimelate transaminase, DapC, beta/gammaproteobacteria / : / 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 ...Succinyldiaminopimelate transaminase, DapC, beta/gammaproteobacteria / : / 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
ACETATE ION / Putative 8-amino-7-oxononanoate synthase / Putative 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesNeisseria meningitidis Z2491 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Aminotransferase (NP_283882.1) from NEISSERIA MENINGITIDIS Z2491 at 1.91 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 / 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.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_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

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Assembly

Deposited unit
A: aminotransferase
B: aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,62316
Polymers89,2462
Non-polymers1,37714
Water12,250680
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-30 kcal/mol
Surface area28760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.617, 116.890, 145.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsCRYSTAL PACKING AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERINGANALYSIS 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 aminotransferase


Mass: 44622.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis Z2491 (bacteria)
Gene: NMA1113, NP_283882.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1IRD6, UniProt: A0A0U1RIH4*PLUS

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Non-polymers , 5 types, 694 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20.0000% polyethylene glycol 8000, 0.2000M calcium acetate, 0.1M MES pH 6.0, Additive: 0.001M pyridoxal-5'-phosphate(PLP), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97922,0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2009 / 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
10.918371
20.979221
30.979361
ReflectionResolution: 1.91→29.311 Å / Num. obs: 74211 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.33 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.55
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.91-1.980.4182.23066014586198.8
1.98-2.060.31433022514251199.1
2.06-2.150.23842913413670199.1
2.15-2.260.1775.32983113938199.3
2.26-2.410.1356.73237215085199.1
2.41-2.590.1018.72979813830199.2
2.59-2.850.07311.63069414225199.1
2.85-3.260.04716.83081214243198.9
3.26-4.10.02925.43069214140198.4
4.1-29.3110.024323090114168197.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.91→29.311 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.478 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.112
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. 2-(N-MORPHOLINO)-ETHANESULFONIC ACID (MES), CALCIUM (CA) ION, ACETATE (ACT) ION, AND GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTIONS ARE MODELED. 5. RESIDUE LYS 244 IS COVALENTLY BONDED TO PYRIDOXAL-5'-PHOSPHATE (PLP) THROUGH A SCHIFF BASE AND HAS BEEN MODELD AS LLP.
RfactorNum. reflection% reflectionSelection details
Rfree0.183 3737 5 %RANDOM
Rwork0.152 ---
obs0.154 74182 99.75 %-
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: 69.49 Å2 / Biso mean: 20.07 Å2 / Biso min: 5.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2--0.17 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.91→29.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6175 0 87 680 6942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226545
X-RAY DIFFRACTIONr_bond_other_d0.0010.024470
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9828930
X-RAY DIFFRACTIONr_angle_other_deg0.894310912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17524.034295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.237151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9031541
X-RAY DIFFRACTIONr_chiral_restr0.0780.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021311
X-RAY DIFFRACTIONr_mcbond_it0.5891.54001
X-RAY DIFFRACTIONr_mcbond_other0.1491.51591
X-RAY DIFFRACTIONr_mcangle_it1.0926467
X-RAY DIFFRACTIONr_scbond_it1.74232544
X-RAY DIFFRACTIONr_scangle_it2.834.52441
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 240 -
Rwork0.194 5174 -
all-5414 -
obs--99.8 %
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)
10.61570.11910.09930.94080.06060.5791-0.06910.0709-0.0559-0.1470.07210.11250.02050.0556-0.00310.07660.00050.00320.07420.00950.035227.49119.046-25.371
20.58860.26080.07780.96110.04560.56080.0493-0.00690.03150.0713-0.0520.016-0.007-0.03560.00280.03730.01130.00110.0550.01840.013337.73933.2956.873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 395
2X-RAY DIFFRACTION2B1 - 395

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