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Basic information

Entry
Database: PDB / ID: 1m3u
TitleCrystal Structure of Ketopantoate Hydroxymethyltransferase complexed the Product Ketopantoate
Components3-methyl-2-oxobutanoate hydroxymethyltransferase
KeywordsTRANSFERASE / beta-alpha-barrel / TIM-barrel / ketopantoate / selenomethionine MAD / decamer
Function / homology
Function and homology information


3-methyl-2-oxobutanoate hydroxymethyltransferase / 3-methyl-2-oxobutanoate hydroxymethyltransferase activity / pantothenate biosynthetic process / magnesium ion binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ketopantoate hydroxymethyltransferase / Ketopantoate hydroxymethyltransferase / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
KETOPANTOATE / 3-methyl-2-oxobutanoate hydroxymethyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
Authorsvon Delft, F. / Inoue, T. / Saldanha, S.A. / Ottenhof, H.H. / Dhanaraj, V. / Witty, M. / Abell, C. / Smith, A.G. / Blundell, T.L.
Citation
Journal: Structure / Year: 2003
Title: Structure of E. coli Ketopantoate Hydroxymethyl Transferase Complexed with Ketopantoate and Mg(2+), Solved by Locating 160 Selenomethionine Sites.
Authors: von Delft, F. / Inoue, T. / Saldanha, S.A. / Ottenhof, H.H. / Schmitzberger, F. / Birch, L.M. / Dhanaraj, V. / Witty, M. / Smith, A.G. / Blundell, T.L. / Abell, C.
#1: Journal: J.Biol.Chem. / Year: 1976
Title: Ketopantoate Hydroxymethyltransferase. I. Purification and Role in Pantothenate Biosynthesis.
Authors: Teller, J.H. / Powers, S.G. / Snell, E.E.
#2: Journal: J.Biol.Chem. / Year: 1976
Title: Ketopantoate Hydroxymethyltransferase. II. Physical, Catalytic, and Regulatory Properties.
Authors: Powers, S.G. / Snell, E.E.
#3: Journal: J.BACTERIOL. / Year: 1993
Title: Cloning and Sequencing of the Escherichia coli panB gene, which encodes ketopantoate hydroxymethyltransferase, and overexpression of the enzyme.
Authors: Jones, C.E. / Brook, J.M. / Buck, D. / Abell, C. / Smith, A.G.
History
DepositionJun 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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.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.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 400COMPOUND TIM-BARREL FOLD WITH 7TH HELIX MISSING; DECAMER WITH 522 POINT SYMMETRY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-methyl-2-oxobutanoate hydroxymethyltransferase
B: 3-methyl-2-oxobutanoate hydroxymethyltransferase
C: 3-methyl-2-oxobutanoate hydroxymethyltransferase
D: 3-methyl-2-oxobutanoate hydroxymethyltransferase
E: 3-methyl-2-oxobutanoate hydroxymethyltransferase
F: 3-methyl-2-oxobutanoate hydroxymethyltransferase
G: 3-methyl-2-oxobutanoate hydroxymethyltransferase
H: 3-methyl-2-oxobutanoate hydroxymethyltransferase
I: 3-methyl-2-oxobutanoate hydroxymethyltransferase
J: 3-methyl-2-oxobutanoate hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,34830
Polymers282,64410
Non-polymers1,70420
Water50,0102776
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30870 Å2
ΔGint-187 kcal/mol
Surface area81760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.074, 157.170, 100.181
Angle α, β, γ (deg.)90.00, 97.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 6 / Auth seq-ID: 3 - 264 / Label seq-ID: 3 - 264

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
DetailsBiological Decamer is Complete in Asymmetric Unit

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Components

#1: Protein
3-methyl-2-oxobutanoate hydroxymethyltransferase / Ketopantoate hydroxymethyltransferase


Mass: 28264.377 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PANB / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): Hfr3000 YA139
References: UniProt: P31057, 3-methyl-2-oxobutanoate hydroxymethyltransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-KPL / KETOPANTOATE / 2-DEHYDROPANTOATE


Mass: 146.141 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H10O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2776 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.8
Details: PEG 8000, sodium chloride, sodium acetate, sodium citrate buffer, pH 6.8, VAPOR DIFFUSION, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19-11 %(v/v)PEG80001reservoir
2100-200 mM1reservoirNaCl
350-100 mMsodium acetate1reservoir
450 mMsodium citrate1reservoirpH6.8
524-32 mg/mlprotein1drop
640 mMketo-pantoate1drop
750 mMHEPES1droppH7.4

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927, 0.9393, 0.979
DetectorType: SBC-2 / Detector: CCD / Date: Aug 26, 1999 / Details: mirror
RadiationMonochromator: Si 220 Double Crystal Si 111 Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979271
20.93931
30.9791
ReflectionResolution: 1.8→75 Å / Num. all: 229086 / Num. obs: 229086 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 12.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.4 / Num. unique all: 26449 / Rsym value: 0.527 / % possible all: 75
Reflection
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 75 % / Rmerge(I) obs: 0.62

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHARPphasing
REFMAC5.1.19refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD
Starting model: Initial C-alpha trace obtained from 3.0 A selenomethionine MAD-phased maps of a different crystal form: P21, cell=(87.8,155.4,209.9,90,99.3,90)

Resolution: 1.8→100 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.974 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Separate TLS groups for each subunit. Individual isotropic temperature factors for all atoms. Overall anisotropic scaling.
Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / ESU R: 0.117 / ESU R Free: 0.114 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. XFIT, SHELXL, O, CNS WERE ALSO USED IN REFINEMENT. Continuous, non-protein density not in the active site has been modelled as water ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. XFIT, SHELXL, O, CNS WERE ALSO USED IN REFINEMENT. Continuous, non-protein density not in the active site has been modelled as water chains, since the true identity was unclear. Of note is the density at the dimer interfaces (i.e. between subunits A/F, B/G, C/H, D/I, E/J) at residues Asp64 and Tyr67. Breakdown of NCS symmetry has been modelled by assigning alternate location indicators (A,B,C) in all chains for the residues concerned: 212-214, 218-228, 234-239. The 'A' flag was assigned to the conformation existing in the majority of chains.
RfactorNum. reflection% reflectionSelection details
Rfree0.19258 4812 2.1 %random
Rwork0.15193 ---
all0.15844 224262 --
obs0.15276 224262 94.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-0.37 Å2
2--0.27 Å20 Å2
3----0.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.115 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19602 0 110 2776 22488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02120424
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218974
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.96927779
X-RAY DIFFRACTIONr_angle_other_deg0.88344006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98352634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.928153307
X-RAY DIFFRACTIONr_chiral_restr0.0920.23242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222990
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023890
X-RAY DIFFRACTIONr_nbd_refined0.2120.24499
X-RAY DIFFRACTIONr_nbd_other0.2370.222355
X-RAY DIFFRACTIONr_nbtor_other0.0850.211372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.22184
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7911.513089
X-RAY DIFFRACTIONr_mcangle_it1.403220946
X-RAY DIFFRACTIONr_scbond_it2.3137335
X-RAY DIFFRACTIONr_scangle_it3.7154.56833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3485 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.295
2Bloose positional0.355
3Cloose positional0.295
4Dloose positional0.295
5Eloose positional0.415
6Floose positional0.245
7Gloose positional0.395
8Hloose positional0.265
9Iloose positional0.35
10Jloose positional0.455
1Aloose thermal2.0310
2Bloose thermal1.9110
3Cloose thermal1.8710
4Dloose thermal1.5310
5Eloose thermal2.1510
6Floose thermal1.3110
7Gloose thermal2.9310
8Hloose thermal1.5310
9Iloose thermal1.9610
10Jloose thermal2.6810
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 309 -
Rwork0.251 11790 -
obs-25768 75 %
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)
10.8754-0.70930.00240.6631-0.25730.9778-0.04660.1031-0.1231-0.11940.00640.2097-0.0283-0.00620.0403-0.0419-0.0196-0.0189-0.13290.0359-0.0721-4.1586.059-4.162
21.0709-0.58160.14322.33370.25560.69130.0509-0.0194-0.2243-0.0772-0.02210.54430.0188-0.3066-0.0287-0.1412-0.0059-0.033-0.09680.0287-0.0367-15.783-21.5517.744
31.8209-0.68580.08180.7088-0.06770.7309-0.1496-0.5661-0.07470.13150.15650.160.0666-0.1783-0.0069-0.13740.03010.02170.07280.007-0.1178-12.237-10.48753.27
41.53130.13350.85550.490.59181.6327-0.178-0.17230.3621-0.00630.0590.0356-0.4199-0.15770.119-0.01420.0641-0.012-0.0496-0.1147-0.01971.16524.09653.371
53.5457-0.2101-0.67780.38160.35490.42920.25730.47661.2404-0.2727-0.01520.0444-0.6338-0.0692-0.24210.3899-0.03420.0785-0.04320.15250.30885.92134.4917.335
61.2671-0.69360.71740.6084-0.25811.50570.08580.40490.1161-0.1807-0.1172-0.19330.05330.4520.0315-0.0790.00530.05280.05540.0126-0.114828.466-10.021-2.892
70.86030.01650.271.33080.19320.1660.00070.1306-0.1205-0.10770.0418-0.12150.090.1189-0.0425-0.10310.01670.0018-0.1298-0.006-0.132517.506-35.86822.503
81.4094-0.1792-0.24430.4425-0.24911.2464-0.1363-0.4007-0.230.12070.1264-0.12610.20610.16940.0098-0.10370.08-0.01390.0581-0.0323-0.080622.532-20.96156.024
91.295-0.50780.00830.5930.27230.6944-0.0652-0.19010.11840.03740.0391-0.0672-0.14160.28560.026-0.1244-0.0542-0.0050.0692-0.1241-0.021335.87913.41852.198
102.1477-2.0189-0.43812.22590.24161.04620.2095-0.11211.0921-0.170.0027-1.1637-0.57990.6458-0.21230.1789-0.30150.14640.1774-0.05820.482739.51220.28614.992
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 2643 - 264
2X-RAY DIFFRACTION2BB3 - 2643 - 264
3X-RAY DIFFRACTION3CC3 - 2643 - 264
4X-RAY DIFFRACTION4DD3 - 2643 - 264
5X-RAY DIFFRACTION5EE3 - 2643 - 264
6X-RAY DIFFRACTION6FF3 - 2643 - 264
7X-RAY DIFFRACTION7GG3 - 2643 - 264
8X-RAY DIFFRACTION8HH3 - 2643 - 264
9X-RAY DIFFRACTION9II3 - 2643 - 264
10X-RAY DIFFRACTION10JJ3 - 2643 - 264
Software
*PLUS
Version: 5.1.995 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor Rfree: 0.196 / Rfactor Rwork: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_d0.0170.2
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.560.02
X-RAY DIFFRACTIONr_plane_restr0.008

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