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- PDB-5cef: Cystal structure of aspartate semialdehyde dehydrogenase from Cry... -

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Basic information

Entry
Database: PDB / ID: 5cef
TitleCystal structure of aspartate semialdehyde dehydrogenase from Cryptococcus neoformans
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / rossman fold
Function / homology
Function and homology information


homoserine biosynthetic process / aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / threonine biosynthetic process / methionine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity
Similarity search - Function
Aspartate-semialdehyde dehydrogenase, peptidoglycan lacking / Aspartate-semialdehyde dehydrogenase, conserved site / 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 ...Aspartate-semialdehyde dehydrogenase, peptidoglycan lacking / Aspartate-semialdehyde dehydrogenase, conserved site / 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
Similarity search - Component
Biological speciesCryptococcus neoformans var. neoformans JEC21 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsDahal, G.P. / Viola, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI077720 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of a fungal form of aspartate semialdehyde dehydrogenase from Cryptococcus neoformans.
Authors: Dahal, G. / Viola, R.E.
History
DepositionJul 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate-semialdehyde dehydrogenase
B: Aspartate-semialdehyde dehydrogenase
C: Aspartate-semialdehyde dehydrogenase
D: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,3265
Polymers161,2644
Non-polymers621
Water11,151619
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-56 kcal/mol
Surface area52570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.590, 130.960, 91.940
Angle α, β, γ (deg.)90.000, 92.870, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 4 - 365 / Label seq-ID: 6 - 367

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Aspartate-semialdehyde dehydrogenase


Mass: 40316.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. neoformans JEC21 (fungus)
Gene: CNA02450 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5KPK7, aspartate-semialdehyde dehydrogenase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 619 / 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: 2.96 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG8000, Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.6→66.05 Å / Num. obs: 55730 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 4.4
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
iMOSFLMdata reduction
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hsk

3hsk


Resolution: 2.6→66.05 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.473 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.605 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 2849 5.1 %RANDOM
Rwork0.1812 ---
obs0.1831 52836 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.76 Å2 / Biso mean: 45.009 Å2 / Biso min: 16.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å20 Å21.87 Å2
2---0.19 Å20 Å2
3----2.78 Å2
Refinement stepCycle: final / Resolution: 2.6→66.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10796 0 4 619 11419
Biso mean--49 40.69 -
Num. residues----1436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911027
X-RAY DIFFRACTIONr_bond_other_d0.0070.0210745
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.96715046
X-RAY DIFFRACTIONr_angle_other_deg1.183324707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44951428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39723.929448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.562151728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9621576
X-RAY DIFFRACTIONr_chiral_restr0.0820.21764
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112560
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022380
X-RAY DIFFRACTIONr_mcbond_it3.5254.2975736
X-RAY DIFFRACTIONr_mcbond_other3.5224.2965735
X-RAY DIFFRACTIONr_mcangle_it5.3486.4337156
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A219160.05
12B219160.05
21A218240.06
22C218240.06
31A216550.07
32D216550.07
41B219260.06
42C219260.06
51B219110.06
52D219110.06
61C218510.06
62D218510.06
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 234 -
Rwork0.248 3875 -
all-4109 -
obs--100 %

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