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- PDB-1dhp: DIHYDRODIPICOLINATE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1dhp
TitleDIHYDRODIPICOLINATE SYNTHASE
ComponentsDIHYDRODIPICOLINATE SYNTHASE
KeywordsSYNTHASE / DIHYDRODIPICOLINATE
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / identical protein binding / cytosol
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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsMirwaldt, C. / Korndoerfer, I. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 A resolution.
Authors: Mirwaldt, C. / Korndorfer, I. / Huber, R.
#1: Journal: Biochem.J. / Year: 1992
Title: Escherichia Coli Dihydrodipicolinate Synthase. Identification of the Active Site and Crystallization
Authors: Laber, B. / Gomis-Ruth, F.X. / Romao, M.J. / Huber, R.
History
DepositionFeb 9, 1995Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _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: DIHYDRODIPICOLINATE SYNTHASE
B: DIHYDRODIPICOLINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6884
Polymers62,6102
Non-polymers782
Water6,197344
1
A: DIHYDRODIPICOLINATE SYNTHASE
B: DIHYDRODIPICOLINATE SYNTHASE
hetero molecules

A: DIHYDRODIPICOLINATE SYNTHASE
B: DIHYDRODIPICOLINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,3768
Polymers125,2204
Non-polymers1564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
MethodPQS
2
A: DIHYDRODIPICOLINATE SYNTHASE
hetero molecules

B: DIHYDRODIPICOLINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6884
Polymers62,6102
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
Buried area3070 Å2
ΔGint-19 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.410, 122.410, 111.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999991, -0.003331, 0.002795), (0.000571, -0.737877, -0.674935), (0.004311, -0.674927, 0.737872)
Vector: 33.7236, 246.8148, 95.7012)

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Components

#1: Protein DIHYDRODIPICOLINATE SYNTHASE / DHDPS


Mass: 31304.936 Da / Num. of mol.: 2 / Mutation: A207T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DAPA / Plasmid: PDB12 / Gene (production host): DAPA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6L2, dihydrodipicolinate synthase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 66 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / Details: Laber, B., (1992) Biochem.J., 288, 691. / PH range low: 10 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.25-3.0 Mammonium salfate1drop
21.25-3.0 Msodium potassium phosphate1drop
30.8-1.6 Msodium citrate1drop
40.2-1.5 Mphosphate1drop
510 %(w/v)PEG60001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Rmerge(I) obs: 0.038

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 2.3→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.197 -
obs0.197 40209
Displacement parametersBiso mean: 23.73 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 2 344 4726
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.662
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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