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- PDB-1vlw: Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4... -

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Basic information

Entry
Database: PDB / ID: 1vlw
TitleCrystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (TM0066) from Thermotoga maritima at 2.30 A resolution
Components2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
KeywordsLYASE / TM0066 / 2-DEHYDRO-3-DEOXYPHOSPHOGLUCONATE ALDOLASE/4-HYDROXY-2-OXOGLUTARATE ALDOLASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


D-galactonate catabolic process / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity
Similarity search - Function
KDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (TM0066) from Thermotoga maritima at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
B: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
C: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase


Theoretical massNumber of molelcules
Total (without water)71,1863
Polymers71,1863
Non-polymers00
Water2,162120
1
A: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase


Theoretical massNumber of molelcules
Total (without water)23,7291
Polymers23,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase


Theoretical massNumber of molelcules
Total (without water)23,7291
Polymers23,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase


Theoretical massNumber of molelcules
Total (without water)23,7291
Polymers23,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
A: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

B: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
C: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase


Theoretical massNumber of molelcules
Total (without water)71,1863
Polymers71,1863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-34 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.543, 113.194, 128.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 4 - 202 / Label seq-ID: 16 - 214

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase


Mass: 23728.762 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0066 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WXS1, 2-dehydro-3-deoxy-phosphogluconate aldolase, 4-hydroxy-2-oxoglutarate aldolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 22.5% PEG-1000, 0.1M Tris pH 7.5 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Jun 12, 2003
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→34.14 Å / Num. obs: 25311 / % possible obs: 97.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 50.2 Å2 / Rsym value: 0.09 / Net I/σ(I): 11.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 1556 / Rsym value: 0.681 / % possible all: 82.2

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Processing

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

1eua


Resolution: 2.3→34.14 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 15.777 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: UNACCOUNTED DENSITY NEXT TO RESIDUE 17,40,69,129 AND 178 IN ALL THREE CHAINS. DISULFIDE BOND BETWEEN CYS165-CYS203 LOOKS PARTIAL WITH ALTERNATE CONFORMATIONS PRESENT BUT UNMODELLED. ...Details: UNACCOUNTED DENSITY NEXT TO RESIDUE 17,40,69,129 AND 178 IN ALL THREE CHAINS. DISULFIDE BOND BETWEEN CYS165-CYS203 LOOKS PARTIAL WITH ALTERNATE CONFORMATIONS PRESENT BUT UNMODELLED. POTENTIAL DISULFIDE BOND BETWEEN CYS76-CYS100. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22106 1286 5.1 %RANDOM
Rwork0.17663 ---
obs0.17887 24015 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.22 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 0 0 120 4770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224744
X-RAY DIFFRACTIONr_bond_other_d0.0010.024485
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9726404
X-RAY DIFFRACTIONr_angle_other_deg0.846310472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61925.029171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.73115850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5521512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025196
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02885
X-RAY DIFFRACTIONr_nbd_refined0.2010.2961
X-RAY DIFFRACTIONr_nbd_other0.1770.24425
X-RAY DIFFRACTIONr_nbtor_other0.0920.22843
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.28
X-RAY DIFFRACTIONr_mcbond_it1.89333177
X-RAY DIFFRACTIONr_mcbond_other0.54231265
X-RAY DIFFRACTIONr_mcangle_it2.81254923
X-RAY DIFFRACTIONr_scbond_it4.73881793
X-RAY DIFFRACTIONr_scangle_it6.578111481
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22276
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1380.21
Refine LS restraints NCS

Ens-ID: 1 / Number: 2925 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.440.5
2Bmedium positional0.60.5
3Cmedium positional0.50.5
1Amedium thermal0.922
2Bmedium thermal0.952
3Cmedium thermal0.932
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 82 5.3 %
Rwork0.274 1466 -
obs--81.05 %
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)
11.0878-0.33050.19882.6459-0.8012.476-0.0729-0.12420.1028-0.06010.0651-0.06580.1212-0.01810.0077-0.08970.04880.0512-0.09930.0179-0.079125.120213.21247.9098
21.1009-0.0616-0.23461.3263-0.38791.8201-0.00180.0332-0.04810.01160.02220.1415-0.0210.2174-0.0205-0.13530.0103-0.0405-0.0574-0.0519-0.082223.996324.74683.687
30.63340.2358-0.12713.0418-0.92592.1237-0.0703-0.1003-0.11660.0557-0.0157-0.01490.0954-0.04160.086-0.04330.04830.0331-0.05070.0251-0.051117.50778.3739113.4198
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 4 - 202 / Label seq-ID: 16 - 214

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC

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