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- PDB-3dnf: Structure of (E)-4-Hydroxy-3-methyl-but-2-enyl Diphosphate Reduct... -

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Basic information

Entry
Database: PDB / ID: 3dnf
TitleStructure of (E)-4-Hydroxy-3-methyl-but-2-enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / trilobal strucure / open alpha/beta / Iron / Iron-sulfur / Isoprene biosynthesis / Metal-binding / NADP
Function / homology
Function and homology information


4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity / dimethylallyl diphosphate biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 4 iron, 4 sulfur cluster binding / metal ion binding
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 / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsRekittke, I.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Structure of (E)-4-Hydroxy-3-methyl-but-2-enyl Diphosphate Reductase, the Terminal Enzyme of the Non-Mevalonate Pathway.
Authors: Rekittke, I. / Wiesner, J. / Demmer, U. / Warkentin, E. / Xu, W. / Troschke, K. / Hintz, M. / No, J.H. / Duin, E.C. / Oldfield, E. / Jomaa, H. / Ermler, U.
History
DepositionJul 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 9, 2020Group: Database references / Derived calculations / Category: struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_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)67,2166
Polymers66,4402
Non-polymers7764
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-42 kcal/mol
Surface area27080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.370, 87.760, 72.400
Angle α, β, γ (deg.)90.00, 95.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33220.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: ispH, lytB, aq_1739 / Plasmid: pASK-AaeoLytB / Production host: Escherichia coli (E. coli) / Strain (production host): TOP 10
References: UniProt: O67625, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 % (w/w) PEG 8000, 0,1 M Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.983 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 1.65→9.9 Å / Num. obs: 78765 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.571 % / Rsym value: 0.045 / Net I/σ(I): 15.94
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 2.356 % / Mean I/σ(I) obs: 3.29 / Num. unique all: 9714 / Rsym value: 0.321 / % possible all: 53.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→9.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.195 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22605 4120 5 %RANDOM
Rwork0.1926 ---
obs0.19429 77992 91.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.247 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20.7 Å2
2--0.1 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.65→9.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 26 561 4999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224610
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9716243
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4095591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01124.877203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37115862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7391527
X-RAY DIFFRACTIONr_chiral_restr0.2490.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023403
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.22300
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23174
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2482
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8831.52933
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32924623
X-RAY DIFFRACTIONr_scbond_it2.2831880
X-RAY DIFFRACTIONr_scangle_it3.4884.51600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 222 -
Rwork0.289 3498 -
obs-3498 57.04 %
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)
13.31710.9957-0.02791.9241-0.23460.4295-0.07110.2723-0.0091-0.09940.0985-0.1332-0.02390.0334-0.0274-0.17060.01710.0294-0.19-0.014-0.221958.75858.471326.8034
29.49261.52462.53784.1512-2.517510.0421-0.51741.23090.7257-0.81620.3972-0.0438-0.8385-0.05170.12020.3549-0.03180.00770.35670.1328-0.169953.526325.35141.3148
32.63171.4142-0.51661.4753-0.42340.38-0.06330.12760.0238-0.05930.0801-0.02570.0496-0.0014-0.0168-0.17880.0139-0.0015-0.1798-0.0005-0.183517.0543-5.817131.351
46.95080.8164-1.52915.33411.16674.7204-0.19211.1851-1.0416-0.62270.1669-0.44860.44210.0030.02520.26480.09310.07130.15-0.20180.079919.7808-31.093116.4116
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA14 - 19514 - 195
2X-RAY DIFFRACTION1AC2302
3X-RAY DIFFRACTION2AA5 - 135 - 13
4X-RAY DIFFRACTION2AA196 - 281196 - 281
5X-RAY DIFFRACTION3BB14 - 19514 - 195
6X-RAY DIFFRACTION3BD3302
7X-RAY DIFFRACTION4BB5 - 135 - 13
8X-RAY DIFFRACTION4BB196 - 282196 - 282

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