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- PDB-2afb: Crystal structure of 2-dehydro-3- deoxygluconokinase (EC 2.7.1.45... -

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Basic information

Entry
Database: PDB / ID: 2afb
TitleCrystal structure of 2-dehydro-3- deoxygluconokinase (EC 2.7.1.45) (tm0067) from THERMOTOGA MARITIMA at 2.05 A resolution
Components2-keto-3-deoxygluconate kinase
KeywordsTRANSFERASE / tm0067 / 2-dehydro-3- deoxygluconokinase / pfkB family carbohydrate kinase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


kinase activity / metal ion binding
Similarity search - Function
Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / : / 2-keto-3-deoxygluconate kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution.
Authors: Mathews, I.I. / McMullan, D. / Miller, M.D. / Canaves, J.M. / Elsliger, M.A. / Floyd, R. / Grzechnik, S.K. / Jaroszewski, L. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, ...Authors: Mathews, I.I. / McMullan, D. / Miller, M.D. / Canaves, J.M. / Elsliger, M.A. / Floyd, R. / Grzechnik, S.K. / Jaroszewski, L. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / McPhillips, T.M. / Morse, A.T. / Quijano, K. / Rife, C.L. / Schwarzenbacher, R. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Weekes, D. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJul 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
SupersessionFeb 28, 2006ID: 1J5V
Revision 1.1Dec 26, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_conn_type.id / _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: 2-keto-3-deoxygluconate kinase
B: 2-keto-3-deoxygluconate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,48412
Polymers78,9712
Non-polymers51210
Water7,098394
1
A: 2-keto-3-deoxygluconate kinase
B: 2-keto-3-deoxygluconate kinase
hetero molecules

A: 2-keto-3-deoxygluconate kinase
B: 2-keto-3-deoxygluconate kinase
hetero molecules

A: 2-keto-3-deoxygluconate kinase
B: 2-keto-3-deoxygluconate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,45136
Polymers236,9146
Non-polymers1,53730
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 area17170 Å2
ΔGint-228 kcal/mol
Surface area65600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.993, 120.993, 260.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-341-

NI

21A-343-

CA

31B-341-

NI

41B-343-

CA

51A-347-

HOH

61A-543-

HOH

71B-349-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: HIS / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 0 - 330 / Label seq-ID: 12 - 342

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

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Components

#1: Protein 2-keto-3-deoxygluconate kinase


Mass: 39485.668 Da / Num. of mol.: 2 / Mutation: 2.7.1.45
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0067 / Production host: Escherichia coli (E. coli) / References: GenBank: 15642842, UniProt: Q9WXS2*PLUS
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.41 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7
Details: 50.0% PEG-200, 0.1M Tris pH 7.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979413, 0.904964, 0.979150
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2001
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794131
20.9049641
30.979151
ReflectionResolution: 2.05→49.69 Å / Num. obs: 45533 / % possible obs: 98.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value% possible all
2.05-2.1689.92.80.3811.959870.38189.9
2.16-2.2998.23.90.3311.462300.331
2.29-2.451005.10.2023.559610.202
2.45-2.651005.10.1375.155870.137
2.65-2.91005.10.095751400.095
2.9-3.241005.10.0817.146610.081
3.24-3.7410050.0668.641470.066
3.74-4.5810050.04911.635150.049
4.58-6.4899.94.90.0461127530.046
6.48-49.6997.94.60.0412.415520.04

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SnBphasing
MLPHAREphasing
CCP4phasing
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→48.63 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 10.753 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.167
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NI SITES WERE ASSIGNED BASED ON ANOMALOUS PEAK HEIGHT, GEOMETRY, AND B-FACTORS. OTHER METALS COULD BE BOUND BUT NI IS MOST PROBABLE. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NI SITES WERE ASSIGNED BASED ON ANOMALOUS PEAK HEIGHT, GEOMETRY, AND B-FACTORS. OTHER METALS COULD BE BOUND BUT NI IS MOST PROBABLE. THE ASSIGNMENT OF CA SITES 7 AND 9 IS BASED ON GEOMETRY, B-FACTOR, AND ANOMALOUS DIFFERENCE FOURIER PEAK HEIGHT. CA SITE 8 AND 10 WERE ASSIGNED BASED ON A SIMILAR ANOMALOUS PEAK HEIGHT AND B-FACTOR. SITE 8 COULD ALSO BE ANOTHER METAL (ZN OR NI) AT LOWER OCCUPANCY. MISSING RESIDUES in Chain A ARE 210-216 AND 332-339, WHILE MISSING RESIDUES IN Chain B ARE 211-216 AND 332-339
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1069 2.3 %RANDOM
Rwork0.176 ---
all0.177 ---
obs0.177 44437 98.07 %-
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: 28.282 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.05→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 10 394 5444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225153
X-RAY DIFFRACTIONr_bond_other_d0.0010.024686
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9436981
X-RAY DIFFRACTIONr_angle_other_deg0.835310815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8925651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36323.568227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11215826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2391529
X-RAY DIFFRACTIONr_chiral_restr0.0930.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021101
X-RAY DIFFRACTIONr_nbd_refined0.2110.21027
X-RAY DIFFRACTIONr_nbd_other0.1780.24568
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22549
X-RAY DIFFRACTIONr_nbtor_other0.0860.22969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2281
X-RAY DIFFRACTIONr_metal_ion_refined0.3060.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4150.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.350.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.216
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3480.21
X-RAY DIFFRACTIONr_mcbond_it2.20233351
X-RAY DIFFRACTIONr_mcbond_other0.70831344
X-RAY DIFFRACTIONr_mcangle_it2.97455178
X-RAY DIFFRACTIONr_scbond_it5.30682094
X-RAY DIFFRACTIONr_scangle_it6.783111803
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4760 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.310.5
MEDIUM THERMAL1.062
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 142 -
Rwork0.254 2836 -
obs--87.69 %
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)
10.8091-0.2414-0.19170.87840.18521.28270.01550.0941-0.0586-0.14090.076-0.13690.11510.1508-0.0915-0.10580.01240.0103-0.0903-0.0564-0.077482.566720.99212.6489
20.6155-0.039-0.01431.30820.64211.8851-0.0153-0.15160.10920.27740.1984-0.2803-0.07030.3453-0.1831-0.056-0.0011-0.0503-0.0244-0.097-0.038181.844949.783836.8975
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-4 - 3318 - 343
22BB0 - 33112 - 343

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