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- PDB-2rij: Crystal structure of a putative 2,3,4,5-tetrahydropyridine-2-carb... -

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Basic information

Entry
Database: PDB / ID: 2rij
TitleCrystal structure of a putative 2,3,4,5-tetrahydropyridine-2-carboxylate n-succinyltransferase (cj1605c, dapd) from campylobacter jejuni at 1.90 A resolution
ComponentsPutative 2,3,4,5-tetrahydropyridine-2-carboxylate N- succinyltransferase
KeywordsTRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytoplasm
Similarity search - Function
Tetrahydrodipicolinate N-succinyltransferase N-terminal / Trimeric LpxA-like enzymes / Alpha-Beta Plaits - #2010 / Type 2 tetrahydrodipicolinate N-succinyltransferase family / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily / Tetrahydrodipicolinate N-succinyltransferase middle / Hexapeptide repeat of succinyl-transferase / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Hexapeptide repeat proteins ...Tetrahydrodipicolinate N-succinyltransferase N-terminal / Trimeric LpxA-like enzymes / Alpha-Beta Plaits - #2010 / Type 2 tetrahydrodipicolinate N-succinyltransferase family / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily / Tetrahydrodipicolinate N-succinyltransferase middle / Hexapeptide repeat of succinyl-transferase / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Trimeric LpxA-like superfamily / 3 Solenoid / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NP_282733.1) from Campylobacter jejuni at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: 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: pdbx_struct_special_symmetry / 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 1.4Jan 25, 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
Remark 999 SEQUENCE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative 2,3,4,5-tetrahydropyridine-2-carboxylate N- succinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2435
Polymers42,8881
Non-polymers3554
Water8,071448
1
A: Putative 2,3,4,5-tetrahydropyridine-2-carboxylate N- succinyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)259,45830
Polymers257,3276
Non-polymers2,13124
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_454y-1/3,x+1/3,-z-2/31
crystal symmetry operation11_564x-y+2/3,-y+4/3,-z-2/31
crystal symmetry operation12_554-x+2/3,-x+y+1/3,-z-2/31
Buried area23300 Å2
MethodPISA
2
A: Putative 2,3,4,5-tetrahydropyridine-2-carboxylate N- succinyltransferase
hetero molecules

A: Putative 2,3,4,5-tetrahydropyridine-2-carboxylate N- succinyltransferase
hetero molecules

A: Putative 2,3,4,5-tetrahydropyridine-2-carboxylate N- succinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,72915
Polymers128,6643
Non-polymers1,06512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area10610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.093, 135.093, 213.742
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-387-

CL

21A-397-

HOH

31A-419-

HOH

41A-444-

HOH

51A-491-

HOH

61A-546-

HOH

71A-633-

HOH

81A-665-

HOH

91A-834-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF BOTH HEXAMER AND TRIMER AS SIGNIFICANT OLIGOMERIZATION STATES IN SOLUTION.

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Components

#1: Protein Putative 2,3,4,5-tetrahydropyridine-2-carboxylate N- succinyltransferase


Mass: 42887.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Serotype O:2 / Gene: NP_282733.1, dapD, Cj1605c / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q0P823, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 448 / 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: 4.38 Å3/Da / Density % sol: 71.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 1.0M Na Citrate, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97957, 0.95373, 0.97942
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2007 / 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
10.979571
20.953731
30.979421
ReflectionResolution: 1.9→29.54 Å / Num. obs: 59121 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 4.1
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.957.50.73246343351.068100
1.95-27.50.93162442090.838100
2-2.067.51.23091441120.643100
2.06-2.127.51.53006039970.508100
2.12-2.197.522925238850.379100
2.19-2.277.52.32814037340.324100
2.27-2.367.52.72732436270.275100
2.36-2.457.532651935180.246100
2.45-2.567.53.52503233200.208100
2.56-2.697.64.22443732330.175100
2.69-2.837.55.22285730280.14100
2.83-37.56.12200529160.114100
3-3.217.56.32036827150.105100
3.21-3.477.46.31883025370.095100
3.47-3.87.47.41725323460.081100
3.8-4.257.48.41581921310.07100
4.25-4.917.47.91397518840.064100
4.91-6.017.47.61185616080.071100
6.01-8.57.28.5921312720.068100
8.5-29.546.86.248357140.0797.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.54 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.196 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.089
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. CITRATE, CL AND GLYCEROL ARE MODELED BASED ON CRYSTALLIZATION AND CRYO CONDITIONS. 5. THERE IS UNMODELED DENSITY NEAR ARG 218.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2991 5.1 %RANDOM
Rwork0.156 ---
obs0.157 59119 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.932 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20.64 Å20 Å2
2--1.28 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 21 448 3373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223070
X-RAY DIFFRACTIONr_bond_other_d0.0010.022095
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9894162
X-RAY DIFFRACTIONr_angle_other_deg0.95335173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9825413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63725.354127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09515564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9511511
X-RAY DIFFRACTIONr_chiral_restr0.0960.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02597
X-RAY DIFFRACTIONr_nbd_refined0.1960.2612
X-RAY DIFFRACTIONr_nbd_other0.1870.22185
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21489
X-RAY DIFFRACTIONr_nbtor_other0.0840.21702
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2318
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.241
X-RAY DIFFRACTIONr_mcbond_it2.27432093
X-RAY DIFFRACTIONr_mcbond_other0.5673800
X-RAY DIFFRACTIONr_mcangle_it3.00553108
X-RAY DIFFRACTIONr_scbond_it5.43981217
X-RAY DIFFRACTIONr_scangle_it7.341111037
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 211 -
Rwork0.259 4105 -
all-4316 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -9.842 Å / Origin y: 59.41 Å / Origin z: -28.889 Å
111213212223313233
T-0.0112 Å2-0.0202 Å20.0136 Å2--0.0492 Å20.0056 Å2---0.0029 Å2
L0.0673 °2-0.0017 °20.0071 °2-0.4448 °2-0.2014 °2--0.4055 °2
S-0.0298 Å °-0.0127 Å °-0.028 Å °0.0249 Å °0.0207 Å °0.0628 Å °0.0982 Å °-0.0427 Å °0.0091 Å °

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