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- PDB-4k57: Structure of Thermus thermophilus 1-pyrroline-5-carboxylate dehyd... -

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Basic information

Entry
Database: PDB / ID: 4k57
TitleStructure of Thermus thermophilus 1-pyrroline-5-carboxylate dehydrogenase R100A mutant
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / ROSSMANN FOLD / NUCLEOTIDE BINDING
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity
Similarity search - Function
1-pyrroline-5-carboxylate dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...1-pyrroline-5-carboxylate dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Delta-1-pyrroline-5-carboxylate dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.537 Å
AuthorsLuo, M.L. / Singh, R.K. / Tanner, J.J.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural determinants of oligomerization of delta (1)-pyrroline-5-carboxylate dehydrogenase: identification of a hexamerization hot spot.
Authors: Luo, M. / Singh, R.K. / Tanner, J.J.
History
DepositionApr 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 20, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Delta-1-pyrroline-5-carboxylate dehydrogenase
B: Delta-1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7224
Polymers114,4862
Non-polymers2362
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-22 kcal/mol
Surface area34830 Å2
MethodPISA
2
A: Delta-1-pyrroline-5-carboxylate dehydrogenase
B: Delta-1-pyrroline-5-carboxylate dehydrogenase
hetero molecules

A: Delta-1-pyrroline-5-carboxylate dehydrogenase
B: Delta-1-pyrroline-5-carboxylate dehydrogenase
hetero molecules

A: Delta-1-pyrroline-5-carboxylate dehydrogenase
B: Delta-1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,16712
Polymers343,4586
Non-polymers7096
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area29490 Å2
ΔGint-90 kcal/mol
Surface area94850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.729, 102.729, 279.509
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Delta-1-pyrroline-5-carboxylate dehydrogenase


Mass: 57243.000 Da / Num. of mol.: 2 / Mutation: R100A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1213 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72IB9, EC: 1.5.1.12
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.05 M citrate, 45% MPD, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.537→47.333 Å / Num. all: 158507 / Num. obs: 158507 / % possible obs: 96.8 % / Redundancy: 5.3 % / Rsym value: 0.045 / Net I/σ(I): 20.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.537-1.622.80.4611.552347187910.46178.5
1.62-1.725.30.3712.1120010225170.37199.5
1.72-1.845.70.233.4121854213050.23100
1.84-1.985.70.135.9113508197880.13100
1.98-2.175.70.0789.9104655182170.078100
2.17-2.435.70.0531493829164540.053100
2.43-2.815.70.04117.282169145190.041100
2.81-3.445.50.03219.368002122910.032100
3.44-4.865.40.02920.25106894460.02999.9
4.86-47.3335.50.02621.52843551790.02699.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BHQ

2bhq


Resolution: 1.537→47.333 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8796 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0.99 / Phase error: 19.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 6989 5.01 %random
Rwork0.1684 ---
obs0.1693 6989 93.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.26 Å2 / Biso mean: 23.0715 Å2 / Biso min: 10.83 Å2
Refinement stepCycle: LAST / Resolution: 1.537→47.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7911 0 16 623 8550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068186
X-RAY DIFFRACTIONf_angle_d1.03911152
X-RAY DIFFRACTIONf_chiral_restr0.0731227
X-RAY DIFFRACTIONf_plane_restr0.0061460
X-RAY DIFFRACTIONf_dihedral_angle_d12.632952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.537-1.55440.29131750.28172758293327
1.5544-1.57270.31382670.27734410467743
1.5727-1.59180.29783830.27256778716166
1.5918-1.6120.28314440.26328479892382
1.612-1.63320.27034920.237295281002092
1.6332-1.65560.26785210.2221103311085298
1.6556-1.67920.23535400.2111102271076799
1.6792-1.70430.24245120.2016103031081599
1.7043-1.73090.22125570.1952103531091099
1.7309-1.75930.22015120.186102691078199
1.7593-1.78960.1954680.18291044910917100
1.7896-1.82220.2095600.18851024510805100
1.8222-1.85720.20854740.1842103381081299
1.8572-1.89510.21515750.1781038310958100
1.8951-1.93640.18365910.17941034110932100
1.9364-1.98140.20165740.17871029510869100
1.9814-2.03090.19145380.17551031410852100
2.0309-2.08590.21325560.16951038610942100
2.0859-2.14720.1875860.16481022010806100
2.1472-2.21650.18315830.16331036110944100
2.2165-2.29580.1935380.15961029910837100
2.2958-2.38770.19115680.16031041110979100
2.3877-2.49630.20685280.16481033510863100
2.4963-2.62790.19765280.16461036410892100
2.6279-2.79260.17795430.16091031710860100
2.7926-3.00820.16015540.16451037910933100
3.0082-3.31080.18545270.16541037410901100
3.3108-3.78970.14975440.1503103421088699
3.7897-4.77390.14415400.13991030010840100
4.7739-47.3330.17245260.16991036910895100

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