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- PDB-5j5d: Crystal structure of Dihydrodipicolinate Synthase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 5j5d
TitleCrystal structure of Dihydrodipicolinate Synthase from Mycobacterium tuberculosis in complex with alpha-ketopimelic acid
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / Dap pathway / L-lysine / alpha-ketopimelic acid
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / plasma membrane / 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
2-oxoheptanedioic acid / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNavratna, V. / Gopal, B.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: Sci Rep / Year: 2016
Title: Inhibition of Mycobacterium tuberculosis dihydrodipicolinate synthase by alpha-ketopimelic acid and its other structural analogues
Authors: Shrivastava, P. / Navratna, V. / Silla, Y. / Dewangan, R.P. / Pramanik, A. / Chaudhary, S. / Rayasam, G. / Kumar, A. / Gopal, B. / Ramachandran, S.
History
DepositionApr 2, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1084
Polymers30,8881
Non-polymers2203
Water1,74797
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,43316
Polymers123,5534
Non-polymers88112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation7_558y,x,-z+31
crystal symmetry operation8_778-y+2,-x+2,-z+31
Buried area10450 Å2
ΔGint-136 kcal/mol
Surface area37330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.780, 84.780, 83.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-541-

HOH

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Components

#1: Protein 4-hydroxy-tetrahydrodipicolinate synthase / Dihydrodipicolinate Synthase


Mass: 30888.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: dapA / Production host: Escherichia coli (E. coli)
References: UniProt: P9WP25, 4-hydroxy-tetrahydrodipicolinate synthase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#3: Chemical ChemComp-6GT / 2-oxoheptanedioic acid / 2-Ketopimelic acid


Mass: 174.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 1.34M tri-sodium citrate, 0.1M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 6.8 % / Number: 83110 / Rsym value: 0.106 / D res high: 2.4 Å / D res low: 59.948 Å / Num. obs: 12296 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
7.5948.7810.0320.0326.3
5.377.5910.0550.0557
4.385.3710.060.067.2
3.794.3810.0690.0697.3
3.393.7910.090.097.3
3.13.3910.1250.1257.3
2.873.110.1750.1757.1
2.682.8710.2510.2516.7
2.532.6810.3180.3186.2
2.42.5310.420.425.7
ReflectionResolution: 2.4→55 Å / Num. all: 12296 / Num. obs: 12296 / % possible obs: 98.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 28.53 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.043 / Rrim(I) all: 0.114 / Rsym value: 0.106 / Net I/σ(I): 13.7 / Num. measured all: 83110
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.535.70.42197.3
7.59-556.30.032199.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
MOSFLMdata collection
SCALA3.3.20data scaling
PHASER2.5.1phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XXX

1xxx


Resolution: 2.4→48.781 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 593 4.83 %RANDOM
Rwork0.1954 ---
obs0.1981 12276 98.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 13 97 2243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042178
X-RAY DIFFRACTIONf_angle_d0.6812966
X-RAY DIFFRACTIONf_dihedral_angle_d14.0721307
X-RAY DIFFRACTIONf_chiral_restr0.043359
X-RAY DIFFRACTIONf_plane_restr0.004389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.64150.30221480.25152794X-RAY DIFFRACTION97
2.6415-3.02370.31111430.24812866X-RAY DIFFRACTION98
3.0237-3.80940.26411490.19262915X-RAY DIFFRACTION99
3.8094-48.79060.19421530.15693108X-RAY DIFFRACTION99
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)
10.3577-0.7098-0.28271.82230.59850.2279-0.03680.31810.2777-0.29020.0865-1.053-0.13510.7126-0.03510.6491-0.04810.33850.52890.11250.7712112.616598.0621104.6818
21.90910.4431-0.30881.8233-0.4731.4167-0.05660.89930.5298-0.8964-0.0501-0.0758-0.59160.1277-0.00070.8015-0.14520.0680.6150.28460.34191.0943102.955297.9298
32.86930.0275-0.0810.3470.4770.6632-0.01980.77570.4831-0.7315-0.0426-0.4692-0.39720.26420.05920.7279-0.34640.28930.78590.29150.3825100.7168102.317597.8196
42.32320.3394-0.5371.0830.02881.382-0.17540.7533-0.2812-0.79240.1727-0.41-0.1240.3640.10610.4976-0.08140.18980.4686-0.03950.289595.647484.3598101.6798
51.1616-1.35270.44151.8157-0.17990.6091-0.08010.93090.142-0.8804-0.1717-0.7396-0.16870.63850.18560.5895-0.09850.36320.8306-0.04170.594105.12384.944698.313
61.72360.4070.13311.1344-0.29581.0055-0.03370.4350.1867-0.3971-0.104-0.5125-0.18630.51740.11450.2844-0.13040.06510.33390.11620.346100.598994.1935114.4891
71.80330.1713-1.91480.67080.79163.4660.03770.22650.5251-0.0532-0.0257-0.4877-0.57540.4349-0.07520.557-0.2585-0.05950.34570.06190.6905103.6994112.2485121.3377
81.4260.2768-0.1971.04830.26251.3206-0.04570.4620.7304-0.4142-0.10950.055-0.6759-0.17510.11150.53920.0253-0.11130.31260.13670.426481.6092108.4162111.5069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:11)
2X-RAY DIFFRACTION2(chain A and resid 12:76)
3X-RAY DIFFRACTION3(chain A and resid 77:88)
4X-RAY DIFFRACTION4(chain A and resid 89:129)
5X-RAY DIFFRACTION5(chain A and resid 130:138)
6X-RAY DIFFRACTION6(chain A and resid 139:223)
7X-RAY DIFFRACTION7(chain A and resid 224:239)
8X-RAY DIFFRACTION8(chain A and resid 240:300)

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