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- PDB-2nuy: 2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius i... -

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Basic information

Entry
Database: PDB / ID: 2nuy
Title2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius in complex with pyruvate
Components2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase
KeywordsLYASE / TIM barrel
Function / homology
Function and homology information


2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / cytosol
Similarity search - Function
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
PYRUVIC ACID / 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
Authorsvan Eerde, A. / Dijkstra, B.W.
CitationJournal: Biochem.J. / Year: 2007
Title: Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases
Authors: Wolterink-van Loo, S. / van Eerde, A. / Siemerink, M.A.J. / Akerboom, J. / Dijkstra, B.W. / van der Oost, J.
History
DepositionNov 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase
B: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3095
Polymers65,1092
Non-polymers2003
Water2,918162
1
A: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase
B: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase
hetero molecules

A: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase
B: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,61910
Polymers130,2184
Non-polymers4016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Unit cell
Length a, b, c (Å)109.090, 109.090, 171.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: x-y,-y,-z+2/3 + (0 1 0)

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Components

#1: Protein 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase


Mass: 32554.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Species: Sulfolobus acidocaldarius / Strain: DSM639 / Gene: saci_0225 / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q4JC35, 2-dehydro-3-deoxy-phosphogluconate aldolase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 4.47 Å3/Da / Density % sol: 72.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG400, 0.1M HEPES, 0.2M Magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 2005
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 41289 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 52.971 Å2 / Rsym value: 0.056 / Net I/σ(I): 17.6
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 5.3 / Num. unique all: 6379 / % possible all: 97.1

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native structure of KDGA

Resolution: 2.5→47.25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 10.899 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: isotropic B factor refinement in combination with TLS refinement
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 2131 5.2 %RANDOM
Rwork0.159 ---
obs0.16 41249 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.73 Å2
Baniso -1Baniso -2Baniso -3
1-3.58 Å21.79 Å20 Å2
2--3.58 Å20 Å2
3----5.38 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4598 0 11 162 4771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224726
X-RAY DIFFRACTIONr_bond_other_d0.0010.023226
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9966407
X-RAY DIFFRACTIONr_angle_other_deg0.84637938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0595574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90524.757206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84615851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7481520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02888
X-RAY DIFFRACTIONr_nbd_refined0.2120.3993
X-RAY DIFFRACTIONr_nbd_other0.1790.33368
X-RAY DIFFRACTIONr_nbtor_refined0.1840.52345
X-RAY DIFFRACTIONr_nbtor_other0.0870.52230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.15303
X-RAY DIFFRACTIONr_metal_ion_refined0.060.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.322
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.1515
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.070.52
X-RAY DIFFRACTIONr_mcbond_it3.6511.53768
X-RAY DIFFRACTIONr_mcbond_other1.1381.51148
X-RAY DIFFRACTIONr_mcangle_it4.22824699
X-RAY DIFFRACTIONr_scbond_it8.14532162
X-RAY DIFFRACTIONr_scangle_it10.474.51708
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 129 -
Rwork0.231 2752 -
obs-2881 95.4 %
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)
11.7620.0595-0.4612.82770.32442.92580.06140.013-0.1735-0.251-0.22040.15090.2051-0.1130.1590.16310.0773-0.0060.1657-0.04610.1593-4.06769.68236.531
20.35340.59720.85731.28790.58264.7690.12170.0537-0.0786-0.1779-0.1259-0.2080.21580.24190.00430.12110.12340.02280.14530.00610.13327.53768.1541.079
30.84821.50162.46689.72757.424621.63230.26560.0421-0.08260.13880.1781-0.7745-0.38220.5147-0.4438-0.00250.034-0.00110.2180.07410.264516.88977.68852.68
42.8137-1.2272-2.07013.7731.7214.78260.37940.12690.117-0.253-0.1746-0.6457-0.27680.2938-0.20480.03360.0420.05090.18480.03960.131312.28178.42343.607
51.8052-2.73290.73515.11420.1721.989-0.02370.18060.4381-0.5761-0.1086-0.8982-0.19080.43750.13230.11920.07120.10330.13650.04250.173810.9187.20537.89
61.12042.10670.37814.36390.11771.0016-0.16510.296-0.0524-0.93040.12930.0028-0.1565-0.09050.03570.29850.1304-0.00780.1503-0.0210.0507-2.86787.84927.285
79.67315.8476-7.15096.0557-5.592613.86550.0180.37840.5932-0.50790.11890.6664-0.6134-1.0143-0.13690.23120.2235-0.12780.0993-0.04590.1087-10.90493.61932.027
82.8296-0.4072-1.04132.78910.50255.55780.11590.0941-0.0799-0.1583-0.15870.3863-0.0855-0.58310.04280.04070.0421-0.0520.1957-0.08370.1622-14.74476.10841.239
914.82230.5503-0.001723.5745-14.701714.13340.1209-0.1853-0.61530.22330.12821.5467-0.1016-1.5786-0.2491-0.11220.1465-0.07240.4023-0.12270.3125-24.47781.10842.073
1016.51625.9017-13.59654.8327-3.950919.0529-0.31731.08780.0228-0.87340.06610.99690.4431-0.80370.25120.1010.2255-0.21910.2386-0.06550.2416-19.27388.16127.198
111.3958-0.5405-0.64191.92121.35754.3350.02880.0908-0.23240.2296-0.1312-0.17810.3690.23620.10240.2031-0.0351-0.01670.12590.05250.17167.51165.04870.133
120.7189-0.65010.67290.86-0.95024.12950.07980.0247-0.18930.2173-0.13180.09570.2968-0.24490.0520.1704-0.09630.04010.1022-0.01730.1273-4.34964.02766.537
1320.112-4.7119-4.372712.02274.0372.21960.34710.63370.3315-0.5193-0.35750.0817-0.744-0.6810.01040.16870.0922-0.02040.31420.01030.0796-8.73580.93851.708
141.45140.8365-0.09123.195-0.04851.91410.24940.1537-0.00740.1478-0.27540.5275-0.0118-0.3680.0260.1174-0.03870.04740.1726-0.02580.1236-9.83775.41164.08
155.8411.2159-0.90745.31842.48053.7225-0.0835-0.02590.19520.3926-0.25920.82820.0843-0.51330.34270.1356-0.0630.04550.1162-0.01250.1279-9.38482.69572.727
160.27550.38260.0571.32461.18691.55890.0001-0.1837-0.11450.4854-0.0314-0.05670.04520.15170.03140.1963-0.0883-0.03380.12970.07620.05185.99180.16279.813
177.5232-2.4193-8.32343.62951.819415.9388-0.1931-0.5533-0.12380.72290.104-0.301-0.3840.95240.08920.2434-0.068-0.17590.17010.040.150912.685.5383.699
185.32071.0073-1.36878.5115-6.408911.67560.12990.31450.13730.1147-0.374-0.57750.01610.73080.24410.156-0.0089-0.07570.26210.0610.268218.56175.32968.541
192.86830.6754-0.27152.95231.24621.96190.14560.1976-0.1180.1207-0.1005-0.62040.15610.8535-0.0451-0.02370.0686-0.09870.20860.09150.205521.26870.8265.869
2016.50040.4381-12.0832.25320.95118.9866-0.5682-0.6364-0.30170.67220.063-1.04870.79230.79750.50510.0633-0.0739-0.23850.26920.04590.207924.17580.5381.668
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 561 - 56
22AA57 - 10457 - 104
33AA105 - 117105 - 117
44AA118 - 142118 - 142
55AA143 - 181143 - 181
66AA182 - 216182 - 216
77AA217 - 232217 - 232
88AA233 - 265233 - 265
99AA266 - 275266 - 275
1010AA276 - 288276 - 288
1111BB1 - 561 - 56
1212BB57 - 10157 - 101
1313BB102 - 110102 - 110
1414BB111 - 142111 - 142
1515BB143 - 173143 - 173
1616BB174 - 208174 - 208
1717BB209 - 233209 - 233
1818BB234 - 248234 - 248
1919BB249 - 273249 - 273
2020BB274 - 288274 - 288

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