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- PDB-3cpr: The crystal structure of Corynebacterium glutamicum dihydrodipico... -

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Basic information

Entry
Database: PDB / ID: 3cpr
TitleThe crystal structure of Corynebacterium glutamicum dihydrodipicolinate synthase to 2.2 A resolution
ComponentsDihydrodipicolinate synthetase
KeywordsLYASE / (beta/alpha)8-barrel fold with a C-terminal alpha-helical segment / Amino-acid biosynthesis / Cytoplasm / Diaminopimelate biosynthesis / Lysine biosynthesis / Schiff base
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytoplasm
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel ...4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsRydel, T.J. / Sturman, E.J. / Rice, E.A.
CitationJournal: Arch.Biochem.Biophys. / Year: 2008
Title: Characterization and crystal structure of lysine insensitive Corynebacterium glutamicum dihydrodipicolinate synthase (cDHDPS) protein.
Authors: Rice, E.A. / Bannon, G.A. / Glenn, K.C. / Jeong, S.S. / Sturman, E.J. / Rydel, T.J.
History
DepositionApr 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0May 30, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_validate_chiral / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_mod_residue.auth_comp_id / _pdbx_struct_mod_residue.label_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.2Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrodipicolinate synthetase
B: Dihydrodipicolinate synthetase


Theoretical massNumber of molelcules
Total (without water)63,2922
Polymers63,2922
Non-polymers00
Water6,990388
1
A: Dihydrodipicolinate synthetase
B: Dihydrodipicolinate synthetase

A: Dihydrodipicolinate synthetase
B: Dihydrodipicolinate synthetase


Theoretical massNumber of molelcules
Total (without water)126,5844
Polymers126,5844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8790 Å2
ΔGint-76 kcal/mol
Surface area41700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.300, 54.810, 98.610
Angle α, β, γ (deg.)90.000, 129.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dihydrodipicolinate synthetase


Mass: 31646.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: dapA / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q546B6, UniProt: P19808*PLUS, dihydrodipicolinate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT RESIDUE 269 IS LEU ACCORDING TO THE DENSITY MAPS.

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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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: protein: 9.1 mg/mL in 20 mM Tris-HCl, pH 8.0, 0.1M KCl, 10 mM pyruvate. precipitant: 24%(w/v) PEG6000, 50 mM NaH2PO4. 10 uL droplets (5uL protein + 5 uL precipitant) suspended over 1mL of ...Details: protein: 9.1 mg/mL in 20 mM Tris-HCl, pH 8.0, 0.1M KCl, 10 mM pyruvate. precipitant: 24%(w/v) PEG6000, 50 mM NaH2PO4. 10 uL droplets (5uL protein + 5 uL precipitant) suspended over 1mL of precipitant solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 28771 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Χ2: 0.991 / Net I/σ(I): 10.6
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.167 / Num. unique all: 2100 / Χ2: 0.751 / % possible all: 70.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
CNXrefinement
RefinementStarting model: PDB entry 1DHP was used to get an initial MR structure solution. A better MR starting solution resulted later when PDB entry 1XXX was made available for use.

1dhp

1xxx


Resolution: 2.2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The active site lysine residues (176a, 176b) form a Schiff base complex with pyruvate. Proline residues 282a, 282b are cis-prolines.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2680 9.4 %10% of data
Rwork0.212 ---
obs0.228 26969 95.7 %-
all-27767 --
Displacement parametersBiso mean: 13.105 Å2
Refine analyzeLuzzati coordinate error obs: 0.313 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 0 388 4806
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.0091.5
X-RAY DIFFRACTIONx_angle_deg1.5162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.2-2.340.25994180.211X-RAY DIFFRACTION4120
2.34-2.520.23754180.1824X-RAY DIFFRACTION4375
2.52-2.770.25964620.2066X-RAY DIFFRACTION4482
2.77-3.170.26154570.2019X-RAY DIFFRACTION4571
3.17-3.990.23454600.1889X-RAY DIFFRACTION4695
3.99-200.2844650.2531X-RAY DIFFRACTION4726
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep_mcl7.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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