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- PDB-6bac: Crystal Structure of Aspartate-Semialdehyde Dehydrogenase from Ne... -

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Basic information

Entry
Database: PDB / ID: 6bac
TitleCrystal Structure of Aspartate-Semialdehyde Dehydrogenase from Neisseria gonorrhoeae
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Aspartate-semialdehyde dehydrogenase / Neisseria gonorrhoeae / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / isoleucine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity
Similarity search - Function
Aspartate-semialdehyde dehydrogenase, gamma-type / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase / Aspartate-semialdehyde dehydrogenase signature. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Aspartate-semialdehyde dehydrogenase, gamma-type / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase / Aspartate-semialdehyde dehydrogenase signature. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / 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
Aspartate-semialdehyde dehydrogenase / Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Aspartate-Semialdehyde Dehydrogenase from Neisseria gonorrhoeae
Authors: Muruthi, M.M. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionOct 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,63710
Polymers40,9091
Non-polymers7299
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.000, 109.000, 72.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Aspartate-semialdehyde dehydrogenase / ASADH / Aspartate-beta-semialdehyde dehydrogenase


Mass: 40908.801 Da / Num. of mol.: 1 / Fragment: NegoA.17885.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: asd, WHOL_00763, WHOL_01676, WHOO_00778, WHOO_02186C / Plasmid: NegoA.17885.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A1D3HC29, UniProt: Q5F5D2*PLUS, aspartate-semialdehyde dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.03 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG1 screen, F11: 25% PEG 3350, 200mM Ammonium Sulfate, HEPES free acid/NaOH pH 7.5: NegoA.17885.a.B1.PW37925 at 21.5mg/ml: cryo: 15% EG: tray 282816F11, puck obs5-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 25, 2017
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→39.539 Å / Num. obs: 29204 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.022 % / Biso Wilson estimate: 39.49 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.077 / Χ2: 1.073 / Net I/σ(I): 13.44 / Num. measured all: 205075 / Scaling rejects: 865
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.156.0410.52.9812989215221500.9210.54699.9
2.15-2.217.0770.4533.4514713209220790.9450.48899.4
2.21-2.287.0020.3145.3514159202920220.970.33899.7
2.28-2.357.2160.334.7214056197219480.9750.35498.8
2.35-2.427.170.265.913802194119250.9870.27999.2
2.42-2.517.2750.2267.1813196183318140.9850.24299
2.51-2.67.2210.1878.212825179417760.9920.299
2.6-2.717.1760.1589.7512250171317070.9930.16999.6
2.71-2.837.2540.14510.1512071167116640.9940.15599.6
2.83-2.977.2480.13112.0911561159615950.9940.1499.9
2.97-3.137.1850.11314.3210842151015090.9940.12299.9
3.13-3.327.1440.09217.4910223143314310.9960.09999.9
3.32-3.557.0450.0723.059496135113480.9970.07699.8
3.55-3.836.8720.06125.898666126212610.9980.06699.9
3.83-4.26.7530.05527.937881116911670.9980.05999.8
4.2-4.76.9050.04831.657278105810540.9980.05299.6
4.7-5.426.9910.04432.1465449379360.9980.04799.9
5.42-6.647.1090.04132.5757308068060.9980.044100
6.64-9.396.9640.03533.9444506396390.9990.037100
9.39-39.5396.2820.03334.323433813730.9970.03697.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UW3

3uw3


Resolution: 2.1→39.539 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.48
RfactorNum. reflection% reflection
Rfree0.2282 1947 6.68 %
Rwork0.1801 --
obs0.1832 29146 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.55 Å2 / Biso mean: 51.4422 Å2 / Biso min: 20.99 Å2
Refinement stepCycle: final / Resolution: 2.1→39.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 41 222 3030
Biso mean--95.58 51.34 -
Num. residues----373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1002-2.15270.2641350.266119462081100
2.1527-2.21090.32551550.26231898205399
2.2109-2.27590.34621250.23571922204799
2.2759-2.34940.31221330.24721900203399
2.3494-2.43330.34091750.23821874204999
2.4333-2.53080.2611550.22841897205299
2.5308-2.64590.25871360.21231917205399
2.6459-2.78540.2641470.204319402087100
2.7854-2.95980.27361340.211619312065100
2.9598-3.18830.27441180.207419752093100
3.1883-3.50890.25341270.184919672094100
3.5089-4.01630.22461460.15619562102100
4.0163-5.05840.15191300.131720032133100
5.0584-39.54560.17341310.156820732204100
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)
15.9739-0.54481.18982.9334-2.43767.6603-0.0066-0.3910.16850.0787-0.1586-0.131-0.36750.2090.13890.2732-0.0483-0.00440.3664-0.03160.218947.2786-34.18661.5399
22.9104-0.75520.20034.0631-1.88526.278-0.2869-0.78570.30550.42410.23310.4236-0.8705-0.72180.05890.44770.0624-0.02870.5889-0.13730.374534.1282-25.22915.1094
32.29031.14061.07931.70120.6941.9758-0.0716-0.11910.3456-0.0318-0.11550.1959-0.3779-0.18680.14640.35540.043-0.0430.3089-0.01320.254726.0165-32.346-19.7116
41.41211.977-3.55522.8453-4.95218.9592-0.0372-0.66640.82880.4318-0.4052-0.9177-0.92191.00640.44181.3708-0.1536-0.15891.2012-0.21551.262246.2916-15.16684.0603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 54 )A-1 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 134 )A55 - 134
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 369 )A135 - 369
4X-RAY DIFFRACTION4chain 'A' and (resid 370 through 371 )A370 - 371

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