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- PDB-3f7t: Structure of active IspH shows a novel fold with a [3Fe-4S] clust... -

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Basic information

Entry
Database: PDB / ID: 3f7t
TitleStructure of active IspH shows a novel fold with a [3Fe-4S] cluster in the catalytic centre
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / pseudo-C3-symmetry / unprecedent fold for FeS-cluster proteins / Iron / Iron-sulfur / Isoprene biosynthesis / Metal-binding / NADP / PROTEIN BINDING
Function / homology
Function and homology information


hydroxymethylbutenyl pyrophosphate reductase activity / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity / dimethylallyl diphosphate biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
4-hydroxy-3-methylbut-2-enyl diphosphate reductase / LytB protein / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain / Rossmann fold - #11270 / Cobalt-precorrin-4 Transmethylase; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / PHOSPHATE ION / PYROPHOSPHATE 2- / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsGraewert, T. / Eppinger, J. / Rohdich, F. / Bacher, A. / Eisenreich, W. / Groll, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Structure of active IspH enzyme from Escherichia coli provides mechanistic insights into substrate reduction.
Authors: Grawert, T. / Rohdich, F. / Span, I. / Bacher, A. / Eisenreich, W. / Eppinger, J. / Groll, M.
History
DepositionNov 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Dec 27, 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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

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Assembly

Deposited unit
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,14914
Polymers72,4462
Non-polymers1,70312
Water7,710428
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0757
Polymers36,2231
Non-polymers8526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0757
Polymers36,2231
Non-polymers8526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.470, 83.470, 215.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 6 / Auth seq-ID: 1 - 310 / Label seq-ID: 13 - 322

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAsymmetric unit contains two biological assemblies; IspH protein is monomeric

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Components

#1: Protein 4-hydroxy-3-methylbut-2-enyl diphosphate reductase /


Mass: 36223.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cytosolic protein / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0029, ispH, JW0027, lytB, yaaE / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: P62623, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6 M Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0,1.7368
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2007 / Details: SILICON OPTICS
RadiationMonochromator: double bounce Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.73681
ReflectionResolution: 1.8→40 Å / Num. all: 78209 / Num. obs: 78209 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 35.16 Å2 / Rmerge(I) obs: 0.075
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.5 / Num. unique all: 10654 / % possible all: 96

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
REFMAC5.2.0019refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.419 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.117 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23823 3898 5 %RANDOM
Rwork0.19898 ---
all0.2 78122 --
obs0.201 74151 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.156 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 0 72 428 5280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224916
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.9776658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7295618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.37524.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.61915854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5691544
X-RAY DIFFRACTIONr_chiral_restr0.3540.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023660
X-RAY DIFFRACTIONr_nbd_refined0.2050.22351
X-RAY DIFFRACTIONr_nbtor_refined0.310.23372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2393
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.220
X-RAY DIFFRACTIONr_mcbond_it0.9461.53155
X-RAY DIFFRACTIONr_mcangle_it1.46824970
X-RAY DIFFRACTIONr_scbond_it2.72731925
X-RAY DIFFRACTIONr_scangle_it4.3774.51682
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2390 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.395
loose thermal1.7310
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 206 -
Rwork0.326 4143 -
obs--73.75 %
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)
11.26010.1268-0.10910.72220.1781.5288-0.04790.0504-0.0929-0.02430.07880.04290.13230.112-0.0309-0.0684-0.0255-0.0086-0.05830.0228-0.08140.88-38.79655.975
20.3889-0.1264-0.24111.37880.31982.43560.10340.02430.07680.00520.066-0.0037-0.27780.1707-0.1694-0.075-0.01360.0593-0.06060.0013-0.048158.31-12.95950.323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 31013 - 322
2X-RAY DIFFRACTION2BB1 - 31013 - 322

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