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- PDB-3zgl: Crystal structures of Escherichia coli IspH in complex with AMBPP... -

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Basic information

Entry
Database: PDB / ID: 3zgl
TitleCrystal structures of Escherichia coli IspH in complex with AMBPP a potent inhibitor of the methylerythritol phosphate pathway
Components4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE
KeywordsOXIDOREDUCTASE / MEP PATHWAY / 4FE-4S CLUSTER
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 / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / 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
Chem-10E / IRON/SULFUR CLUSTER / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsBorel, F. / Barbier, E. / Kratsutsky, S. / Janthawornpong, K. / Rohmer, M. / Dale Poulter, C. / Ferrer, J.L. / Seemann, M.
CitationJournal: Chembiochem / Year: 2017
Title: Further Insight into Crystal Structures of Escherichia coli IspH/LytB in Complex with Two Potent Inhibitors of the MEP Pathway: A Starting Point for Rational Design of New Antimicrobials.
Authors: Borel, F. / Barbier, E. / Krasutsky, S. / Janthawornpong, K. / Chaignon, P. / Poulter, C.D. / Ferrer, J.L. / Seemann, M.
History
DepositionDec 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_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: 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)74,5056
Polymers73,2792
Non-polymers1,2254
Water14,574809
1
A: 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2523
Polymers36,6401
Non-polymers6132
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)37,2523
Polymers36,6401
Non-polymers6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.120, 80.650, 71.090
Angle α, β, γ (deg.)90.00, 94.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2144-

HOH

21B-2119-

HOH

31B-2120-

HOH

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Components

#1: Protein 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE / ISPH / (E)-4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE (E)-4-AMINO-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE


Mass: 36639.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: P62623, EC: 1.17.1.2
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-10E / (2E)-4-amino-3-methylbut-2-en-1-yl trihydrogen diphosphate


Mass: 261.107 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13NO7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 2.34 Å3/Da / Density % sol: 47.5 % / Description: NONE
Crystal growpH: 6.5 / Details: 24% PEG 3350, 0.1 M BIS-TRIS PH6.5, 200 MM LISO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→46.96 Å / Num. obs: 68152 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.7
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KE8

3ke8


Resolution: 1.68→46.96 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.996 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24179 3408 5 %RANDOM
Rwork0.18725 ---
obs0.19001 64744 94.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.073 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å20.27 Å2
2---2.97 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.68→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4753 0 46 809 5608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194981
X-RAY DIFFRACTIONr_bond_other_d0.0020.024810
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.9736781
X-RAY DIFFRACTIONr_angle_other_deg1.7583.00211042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2165640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14624.174230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22715862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.931545
X-RAY DIFFRACTIONr_chiral_restr0.1310.2780
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215721
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021096
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr12.06939789
X-RAY DIFFRACTIONr_sphericity_free20.8995175
X-RAY DIFFRACTIONr_sphericity_bonded9.13310335
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 244 -
Rwork0.196 4643 -
obs--93.37 %
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)
10.09130.146-0.12830.2686-0.21180.5236-0.0115-0.0213-0.0248-0.0351-0.00880.01230.05760.0070.02030.0271-0.0035-0.01930.1166-0.0030.107537.1578-9.923629.426
22.56951.9853-0.69512.58270.59751.41610.08830.02290.13140.1395-0.17850.21060.0612-0.21860.09020.01160.00090.00460.1436-0.01740.107625.4469-8.516539.5043
30.07010.17810.08150.5057-0.00931.04340.051-0.01920.01660.1394-0.06670.0455-0.021-0.01040.01570.0484-0.02340.00990.1355-0.01310.099336.94433.997143.6154
40.11670.0509-0.08070.64250.03580.06670.0175-0.00780.02730.0179-0.00150.0443-0.00290.0016-0.0160.0271-0.0019-0.0130.1158-0.00230.089840.961617.650631.2842
50.0210.0069-0.06950.49890.05880.4494-0.01660.0062-0.0066-0.07140.00470.0245-0.00510.00510.01190.0402-0.0063-0.01930.1117-0.00120.088139.7666-4.284110.6526
60.66940.41590.18190.2948-0.04631.04650.0973-0.019-0.1480.0608-0.0605-0.0654-0.04280.1793-0.03680.03020.0199-0.03210.1423-0.0090.121850.5117-8.575928.2867
70.2293-0.02930.19740.23910.00070.3235-0.015-0.01480.02150.0255-0.0017-0.0503-0.01610.00510.01670.0251-0.0026-0.02690.1180.00010.096318.50798.77163.6771
80.00890.08020.01491.34840.09270.61610.01090.01640.00650.2116-0.0054-0.07730.0762-0.0433-0.00550.0635-0.0061-0.03030.11430.00620.085814.4302-12.92016.9049
90.00970.0615-0.02110.4267-0.11930.2414-0.00410.00040.00090.0050.0056-0.03240.0599-0.0061-0.00140.0418-0.005-0.00670.11740.00040.092810.8641-16.542-4.8855
100.21-0.02540.00680.49670.03870.3898-0.01190.03170.0016-0.05350.0092-0.0987-0.01660.00020.00270.0296-0.00590.00670.1154-0.00220.099318.216.2973-21.9744
118.05344.2666-4.64032.416-2.53292.9209-0.05880.15930.4128-0.02460.17730.1238-0.043-0.277-0.11860.03590.0371-0.04940.1965-0.05040.13373.36049.9814-21.8051
122.37091.08711.9072.07662.75443.7910.0746-0.30550.28630.0687-0.0681-0.07620.1177-0.169-0.00650.0257-0.0042-0.00340.1538-0.02930.1434.536711.16554.0896
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 49
2X-RAY DIFFRACTION2A50 - 69
3X-RAY DIFFRACTION3A70 - 112
4X-RAY DIFFRACTION4A113 - 204
5X-RAY DIFFRACTION5A205 - 288
6X-RAY DIFFRACTION6A289 - 309
7X-RAY DIFFRACTION7B1 - 101
8X-RAY DIFFRACTION8B102 - 140
9X-RAY DIFFRACTION9B141 - 206
10X-RAY DIFFRACTION10B207 - 287
11X-RAY DIFFRACTION11B288 - 297
12X-RAY DIFFRACTION12B298 - 309

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