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- PDB-1vm6: Crystal structure of Dihydrodipicolinate reductase (TM1520) from ... -

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Basic information

Entry
Database: PDB / ID: 1vm6
TitleCrystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution
ComponentsDihydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / TM1520 / DIHYDRODIPICOLINATE REDUCTASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase activity / : / : / NAD binding / NADP binding / cytosol
Similarity search - Function
Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
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
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
C: Dihydrodipicolinate reductase
D: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,10125
Polymers100,9004
Non-polymers4,20121
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17840 Å2
ΔGint-71 kcal/mol
Surface area33320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.077, 109.217, 112.602
Angle α, β, γ (deg.)90.00, 119.23, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPHEPHEAA1 - 9813 - 110
21METMETPHEPHEBB1 - 9813 - 110
31METMETPHEPHECC1 - 9813 - 110
41METMETPHEPHEDD1 - 9813 - 110
12SERSERILEILEAA99 - 182111 - 194
22SERSERILEILEBB99 - 182111 - 194
32SERSERILEILECC99 - 182111 - 194
42SERSERILEILEDD99 - 182111 - 194
13SERSERILEILEAA183 - 212195 - 224
23SERSERILEILEBB183 - 212195 - 224
33SERSERILEILECC183 - 212195 - 224
43SERSERILEILEDD183 - 212195 - 224

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dihydrodipicolinate reductase / DHPR


Mass: 25225.061 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: dapB, TM1520 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1K8, EC: 1.3.1.26

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Non-polymers , 5 types, 550 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 3.38 Å3/Da / Density % sol: 63.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.5
Details: 20.0% PEG-400, 0.2M Ca(OAc)2, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.980075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2004 / Details: flat mirror
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980075 Å / Relative weight: 1
ReflectionResolution: 2.27→29.03 Å / Num. obs: 61963 / % possible obs: 47.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 46.59 Å2 / Rsym value: 0.086 / Net I/σ(I): 10.8
Reflection shellResolution: 2.27→2.39 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Num. unique all: 7228 / Rsym value: 0.507 / % possible all: 38.4

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.2.0005refinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1arz

1arz


Resolution: 2.27→29.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 10.618 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21256 3151 5.1 %RANDOM
Rwork0.17127 ---
obs0.17334 58811 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.509 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å2-0.6 Å2
2--0.29 Å20 Å2
3----2.64 Å2
Refinement stepCycle: LAST / Resolution: 2.27→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6730 0 275 529 7534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227142
X-RAY DIFFRACTIONr_bond_other_d0.0030.026640
X-RAY DIFFRACTIONr_angle_refined_deg1.5962.0089642
X-RAY DIFFRACTIONr_angle_other_deg0.919315462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81624.216287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.438151241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9571532
X-RAY DIFFRACTIONr_chiral_restr0.0890.21095
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027671
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021333
X-RAY DIFFRACTIONr_nbd_refined0.1960.21370
X-RAY DIFFRACTIONr_nbd_other0.1770.26699
X-RAY DIFFRACTIONr_nbtor_other0.0860.24282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2436
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.221
X-RAY DIFFRACTIONr_mcbond_it1.23734646
X-RAY DIFFRACTIONr_mcbond_other0.52631785
X-RAY DIFFRACTIONr_mcangle_it1.74256938
X-RAY DIFFRACTIONr_scbond_it3.93683071
X-RAY DIFFRACTIONr_scangle_it5.093112704
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23359
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A575tight positional0.050.05
12B575tight positional0.070.05
13C575tight positional0.050.05
14D575tight positional0.040.05
11A915medium positional0.590.5
12B915medium positional0.870.5
13C915medium positional0.610.5
14D915medium positional0.560.5
11A575tight thermal0.090.5
12B575tight thermal0.150.5
13C575tight thermal0.10.5
14D575tight thermal0.10.5
11A915medium thermal0.62
12B915medium thermal0.912
13C915medium thermal0.732
14D915medium thermal0.722
21A493tight positional0.060.05
22B493tight positional0.090.05
23C493tight positional0.090.05
24D493tight positional0.090.05
21A788medium positional0.710.5
22B788medium positional0.90.5
23C788medium positional0.850.5
24D788medium positional0.770.5
21A493tight thermal0.130.5
22B493tight thermal0.150.5
23C493tight thermal0.140.5
24D493tight thermal0.160.5
21A788medium thermal0.822
22B788medium thermal0.952
23C788medium thermal12
24D788medium thermal0.892
31A176tight positional0.080.05
32B176tight positional0.090.05
33C176tight positional0.10.05
34D176tight positional0.060.05
31A272medium positional0.640.5
32B272medium positional0.650.5
33C272medium positional0.890.5
34D272medium positional0.630.5
31A176tight thermal0.110.5
32B176tight thermal0.120.5
33C176tight thermal0.160.5
34D176tight thermal0.110.5
31A272medium thermal0.892
32B272medium thermal0.922
33C272medium thermal1.032
34D272medium thermal0.712
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 185 5.43 %
Rwork0.261 3220 -
obs--71.93 %
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)
13.91680.0448-0.40414.6471-0.03553.7069-0.02020.05130.59710.45110.24340.3464-0.7693-0.6104-0.22320.14090.2260.1105-0.02570.1842-0.021412.995734.103723.6416
22.7191-0.479-0.43043.36811.13353.4248-0.1642-0.18520.14780.09740.10690.0281-0.3812-0.07450.0573-0.32450.062-0.0113-0.27980.0059-0.208824.112212.779359.9664
35.08732.2945-0.48625.7868-0.79885.8735-0.43590.5899-0.6593-0.95940.5106-0.43251.1435-0.105-0.07480.1902-0.320.0988-0.0555-0.1711-0.017815.1416-36.235420.7533
42.7967-1.2484-0.70134.09031.70996.59550.0270.0815-0.2094-0.08660.168-0.35860.58010.7964-0.195-0.1217-0.05020.0369-0.0645-0.1316-0.104650.0445-17.18829.6694
50.9774-0.2524-0.06554.0484-0.19040.526-0.00490.28640.0785-0.19640.1704-0.1465-0.3275-0.3134-0.1655-0.1522-0.0056-0.0474-0.06550.0963-0.187421.322914.637718.2619
60.8702-0.2977-0.59611.21761.37583.5062-0.14550.0709-0.1130.10460.04050.17440.091-0.32560.1049-0.3425-0.0175-0.0155-0.24180.0462-0.181823.202-1.109843.2625
70.330.23030.02923.2387-0.49030.9069-0.15230.2138-0.1314-0.1320.18310.27020.0909-0.3745-0.0308-0.2659-0.1488-0.0348-0.0282-0.0064-0.101213.1507-12.01927.3297
81.1828-1.234-0.92692.3881.43823.112-0.01650.2508-0.0199-0.42650.1102-0.1657-0.3275-0.0058-0.0937-0.2478-0.143-0.0256-0.1738-0.0255-0.199238.5577-0.899318.3246
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 9913 - 111
22BB1 - 9913 - 111
33CC1 - 9913 - 111
44DD1 - 9913 - 111
55AA101 - 212113 - 224
66BB101 - 212113 - 224
77CC101 - 212113 - 224
88DD101 - 212113 - 224

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