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- PDB-2hmc: The Crystal Structure of Dihydrodipicolinate Synthase DapA from A... -

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Basic information

Entry
Database: PDB / ID: 2hmc
TitleThe Crystal Structure of Dihydrodipicolinate Synthase DapA from Agrobacterium tumefaciens
ComponentsDihydrodipicolinate synthase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta Barrel (TIM barrel) / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase activity / metal ion binding
Similarity search - Function
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
Dihydrodipicolinate synthase / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKim, Y. / Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2006
Title: The Crystal Structure of Dihydrodipicolinate Synthase DapA from Agrobacterium tumefaciens
Authors: Kim, Y. / Zhang, R. / Xu, X. / Zheng, H. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionJul 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_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.pdbx_leaving_atom_flag / _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_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: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6883
Polymers37,6391
Non-polymers492
Water7,368409
1
A: Dihydrodipicolinate synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)226,12718
Polymers225,8356
Non-polymers29212
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_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area16050 Å2
ΔGint-143 kcal/mol
Surface area65390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.102, 101.102, 120.914
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-585-

HOH

21A-610-

HOH

31A-650-

HOH

41A-688-

HOH

51A-874-

HOH

Detailshexamer the asymmetric unit contains a monomer and the others are generated by -x+y, y,-z+1/2 y,1-x+y,z+1/2 1-x+y,1-x,z -x,1-x+y,-z 1+y,1+x,-z

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Components

#1: Protein Dihydrodipicolinate synthase / AGR_L_411p


Mass: 37639.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: dapA / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q8U6Y1, UniProt: A9CGZ4*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2M Tri-Lithium Citrate, 20% PEG3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 22, 2006 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→31.92 Å / Num. all: 29275 / Num. obs: 29211 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 25.6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 18.6 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1404 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→31.92 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.98 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.167
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.24674 2813 10 %RANDOM
Rwork0.18715 ---
all0.19315 25301 --
obs0.19315 25301 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.017 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20.83 Å20 Å2
2--1.67 Å20 Å2
3----2.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 2 409 2799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222577
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9543506
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8155339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23523.333108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97515428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2091517
X-RAY DIFFRACTIONr_chiral_restr0.0990.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021982
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21416
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21811
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2333
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8991.51674
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25222630
X-RAY DIFFRACTIONr_scbond_it2.30531023
X-RAY DIFFRACTIONr_scangle_it3.5494.5876
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 212 -
Rwork0.311 1826 -
obs-1826 96.4 %
Refinement TLS params.Method: refined / Origin x: 4.0667 Å / Origin y: 34.1192 Å / Origin z: 12.2766 Å
111213212223313233
T-0.0328 Å20.0216 Å20.0175 Å2--0.0682 Å2-0.0289 Å2---0.0491 Å2
L0.3981 °20.0661 °2-0.0036 °2-0.4883 °2-0.0966 °2--0.7184 °2
S-0.0296 Å °0.0332 Å °-0.0977 Å °-0.1077 Å °-0.0088 Å °-0.0189 Å °0.2223 Å °0.0162 Å °0.0384 Å °

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