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- PDB-4mv0: IspH in complex with pyridin-2-ylmethyl diphosphate -

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Basic information

Entry
Database: PDB / ID: 4mv0
TitleIspH in complex with pyridin-2-ylmethyl diphosphate
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / Iron-sulfur cluster / Reductase / pyridin-2-ylmethyl diphosphate / Cytosol
Function / homology4-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 / pyridin-2-ylmethyl trihydrogen diphosphate / FE3-S4 CLUSTER / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSpan, I. / Wang, K. / Song, Y. / Eisenreich, W. / Bacher, A. / Oldfield, E. / Groll, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Insights into the Binding of Pyridines to the Iron-Sulfur Enzyme IspH.
Authors: Span, I. / Wang, K. / Eisenreich, W. / Bacher, A. / Zhang, Y. / Oldfield, E. / Groll, M.
History
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Sep 20, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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: 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)73,3466
Polymers72,2162
Non-polymers1,1304
Water4,432246
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6733
Polymers36,1081
Non-polymers5652
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)36,6733
Polymers36,1081
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.470, 80.800, 111.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999843, 0.009452, 0.014959), (0.009327, 0.999921, -0.008436), (-0.015037, -0.008295, -0.999853)-65.5236, 0.3302, -0.31311

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Components

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


Mass: 36107.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: ECDH1ME8569_0026, ispH / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue
References: UniProt: C9QSC3, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical ChemComp-2E6 / pyridin-2-ylmethyl trihydrogen diphosphate


Mass: 269.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NO7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 0.1 M BIS-TRIS, 0.2 M ammonium sulfate, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2012
RadiationMonochromator: double-crystal fixed-exit monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 50202 / Num. obs: 49549 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rsym value: 0.09 / Net I/σ(I): 11.37
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 2.82 / Rsym value: 0.421 / % possible all: 95.6

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KE8
Resolution: 1.9→14.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.504 / SU ML: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflection
Rfree0.256 2472 5 %
Rwork0.218 --
obs0.22 49441 98.5 %
all-47666 -
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 36.53 Å2
Baniso -1Baniso -2Baniso -3
1--3.43 Å20 Å2-0 Å2
2--3.32 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 46 246 5065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194895
X-RAY DIFFRACTIONr_bond_other_d0.0010.024751
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9766636
X-RAY DIFFRACTIONr_angle_other_deg0.744310900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4555617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24424.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49115853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1981544
X-RAY DIFFRACTIONr_chiral_restr0.0950.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215553
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021075
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_it0.9851.572474
X-RAY DIFFRACTIONr_mcbond_other0.9831.5692473
X-RAY DIFFRACTIONr_mcangle_it1.7122.3483089
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_restr4.97439646
X-RAY DIFFRACTIONr_sphericity_free29.692578
X-RAY DIFFRACTIONr_sphericity_bonded16.27959747
LS refinement shellResolution: 1.9→1.95 Å
RfactorNum. reflection% reflection
Rfree0.375 171 -
Rwork0.365 3245 -
obs--95.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.4502-2.2854-0.50512.26720.57480.9931-0.1044-0.26460.0760.10250.1751-0.4230.12920.274-0.07070.11940.026-0.00490.3224-0.00010.2975-6.9556-8.855-7.6847
24.72091.11092.52851.07730.60241.43140.11320.0185-0.3227-0.0073-0.0039-0.04530.145-0.0493-0.10930.1264-0.00880.02420.2731-0.00150.229-29.6721-9.8978-10.8036
32.1863-0.28481.12422.19390.99814.8274-0.0691-0.0336-0.0977-0.69770.0730.32280.0948-0.1212-0.00380.319-0.0103-0.05390.3288-0.01260.3506-40.1656-13.4993-21.2635
42.3854-1.88580.36654.0603-0.29730.52050.18040.1933-0.1389-0.3437-0.1472-0.0760.07250.0871-0.03320.1831-0.0035-0.01810.31520.01120.2835-26.9623-10.1363-21.2512
55.3919-3.68611.6996.22221.59582.61330.45680.27770.1619-0.8905-0.4147-0.3225-0.2615-0.116-0.04210.29980.0035-0.0020.36980.0470.2893-37.6828-10.1561-27.5076
60.7112-0.0937-0.19363.93791.22840.42150.018-0.00010.022-0.1178-0.140.4274-0.0376-0.04940.1220.1735-0.0216-0.02080.34660.02130.283-41.2196-5.2744-20.4907
73.38071.97491.79792.49943.28344.6655-0.11440.22150.3959-0.05010.04450.1626-0.0232-0.04820.06990.23890.0278-0.09170.40210.01140.4385-48.448-0.2483-22.0419
81.6595-0.9925-1.01174.4455-1.61751.9026-0.01460.0913-0.1207-0.0423-0.00170.22090.0362-0.09440.01620.02680.0166-0.00710.2996-0.02690.2662-38.6622-0.4272-11.4515
95.1644-0.3869-2.04914.10114.63045.73550.3296-0.1620.71080.1264-0.27440.14720.0437-0.2619-0.05520.07890.03220.04520.4828-0.03830.4979-43.719714.9466-9.0266
100.62181.41110.11734.19671.91862.8062-0.15020.06020.0491-0.48370.14250.0779-0.1132-0.05410.00780.11930.01790.01410.32410.00370.2679-30.812812.0608-17.5399
110.15940.5043-0.15012.214-0.52280.1575-0.00280.04550.066-0.20210.03930.2522-0.0171-0.0442-0.03650.17590.024-0.03030.3896-0.01340.3474-34.475320.9732-16.4396
120.9193-0.5452-0.57194.48550.05430.38230.0244-0.02370.08480.03130.0037-0.0728-0.0420.0121-0.02810.11080.0185-0.00220.29610.00090.2437-24.528814.1736-10.2743
130.50040.8178-0.38654.3579-2.52421.49180.0013-0.01370.03930.08110.0156-0.0106-0.0164-0.0234-0.01690.19290.00410.00620.36870.00560.3293-29.10422.6824-5.3849
143.1215-1.33680.28621.4208-0.85920.68420.029-0.06590.23010.079-0.0716-0.1727-0.04330.09710.04260.12570.0081-0.00780.2634-0.00690.2358-18.86622.6711-6.0201
152.11730.3279-0.03522.11560.02970.9122-0.03710.00560.00260.08270.0064-0.1581-0.0420.12630.03070.12250.0090.00930.28480.00830.2358-11.29640.2262-15.7586
162.0170.7007-0.15040.76310.77032.683-0.03810.1855-0.0929-0.17130.1348-0.1526-0.14580.2245-0.09670.18440.00650.01660.33080.0020.3572-2.4688-8.6556-20.4795
171.5983-0.4422-0.21811.38630.97940.95680.15540.0172-0.2157-0.016-0.0314-0.12490.21390.0675-0.12410.21210.03240.00490.30890.00250.2592-14.6596-11.7163-13.6847
180.8636-0.8967-1.49531.26951.49953.675-0.1135-0.0477-0.04110.06330.0596-0.01790.21850.20830.05390.1594-0.0270.00090.35770.00210.3319-7.419-11.6588-7.9851
197.06730.0354.01380.00780.11763.99190.0265-0.0005-0.2610.0113-0.001-0.0028-0.0409-0.1366-0.02560.12890.00510.0060.2716-0.00880.2541-31.4835-7.3904-2.1862
201.4788-2.7628-2.653817.25258.36765.7252-0.10040.1285-0.003-0.0708-0.00310.38660.1011-0.18550.10350.1392-0.01410.00520.45070.00380.3755-44.2215-13.354-7.603
215.85731.8575-0.26381.54290.4621.4149-0.15570.3052-0.3039-0.0495-0.00550.3720.0966-0.38720.16110.0842-0.02440.00320.3280.00440.3788-58.4234-8.64218.3797
221.2746-0.44420.45021.1018-0.080.96920.005-0.1192-0.07470.09810.0092-0.05230.12910.0216-0.01420.1149-0.0082-0.00020.2820.00320.2561-33.2478-10.971617.702
239.5920.41641.60519.9799-4.44132.40340.17610.28010.06660.05760.07310.20720.2303-0.0302-0.24920.5457-0-0.13740.3886-0.00760.3201-33.3799-17.608225.3065
240.6789-0.15410.61840.5536-0.38160.6846-0.0155-0.0783-0.03940.2188-0.0116-0.0651-0.1042-0.01340.02710.14280.0107-0.01140.35170.01060.2971-24.3404-6.128524.6953
254.0501-2.0719-2.18971.07821.29122.8182-0.12060.0869-0.14640.0170.01740.0709-0.43660.35770.10320.1935-0.0327-0.02510.3987-0.0130.4001-17.99342.378320.43
260.6927-0.128-0.17560.2876-0.58251.63840.19960.10260.1636-0.1351-0.2056-0.12630.2870.30910.0060.18090.0357-0.03210.35420.05090.3233-23.0309-3.98315.878
2712.76765.95120.853.13531.05341.3128-0.1350.59230.2011-0.28720.2231-0.0279-0.38340.0582-0.08820.19060.05790.0820.44090.15770.4875-23.630611.92768.5426
280.916-0.40591.16455.070.30771.6275-0.03830.00930.0031-0.17080.08820.0136-0.01330.0404-0.050.1280.0051-0.01030.3201-0.01140.2809-33.005913.303516.935
292.906-0.67291.61055.6525-3.20872.35590.1005-0.16070.20380.1949-0.3893-0.4435-0.04190.1250.28880.09390.0058-0.02220.4255-0.06290.4458-23.502614.81517.9403
300.4590.2119-0.30271.937-0.35060.5490.0273-0.05770.22810.0929-0.0343-0.115-0.2040.06160.0070.1568-0.0141-0.01080.3136-0.01060.2863-36.842519.882413.4882
310.2490.4539-0.00231.19250.89832.233-0.112-0.0231-0.0154-0.2883-0.00910.0134-0.19640.0770.12110.1620.0191-0.01330.3754-0.01820.3167-36.11422.77495.3632
324.35410.4395-0.19892.60440.58080.19880.18660.13770.00530.0135-0.10720.0497-0.0666-0.0614-0.07940.12520.01010.03440.26520.01720.2186-44.10583.08846.3967
336.57323.6279-4.89378.8086-3.59059.79080.30630.03650.23550.1051-0.14390.1884-0.4259-0.1989-0.16230.12590.0095-0.0140.3364-0.01360.324-59.75650.33368.3067
343.8761-0.77420.74362.0488-0.59691.1182-0.0906-0.2180.0780.15450.00630.1833-0.0996-0.07390.08430.1356-0.00340.0080.2854-0.02960.1991-49.33330.223217.3501
350.55190.1653-0.1281.8668-0.05050.0309-0.03510.0329-0.0428-0.01770.0490.2750.0001-0.0118-0.01390.2169-0.00160.01430.37590.00020.3211-56.58780.051817.9039
365.5147-1.53980.59960.4511-0.49995.8664-0.1133-0.1418-0.05770.03020.04630.03270.3102-0.11970.0670.1563-0.04320.05190.33220.00610.5098-63.7227-8.012521.1623
371.71090.024-0.56631.6186-0.0310.49710.0175-0.0047-0.2060.0630.04340.17980.2252-0.0606-0.06090.1958-0.0247-0.03840.29860.0050.2569-50.758-11.459614.0744
382.92921.3853-2.81651.2843-2.61975.8101-0.0427-0.0123-0.0101-0.07210.07830.10840.0643-0.2033-0.03560.13670.00540.00320.3268-0.02140.3479-57.9596-11.40558.6305
395.3989-0.52192.60170.1888-0.032.860.00030.1569-0.11230.0177-0.0472-0.05630.23360.12770.04690.0881-0.01460.01690.28820.00580.2564-32.8718-7.67463.1466
403.9587-8.0192-0.432427.5771-0.27331.0302-0.22240.01280.1447-0.8130.1377-0.92870.78690.26880.08470.62330.18170.05960.5454-0.02070.2206-22.1069-15.29187.8014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 24
3X-RAY DIFFRACTION3A25 - 37
4X-RAY DIFFRACTION4A38 - 49
5X-RAY DIFFRACTION5A50 - 64
6X-RAY DIFFRACTION6A65 - 77
7X-RAY DIFFRACTION7A78 - 89
8X-RAY DIFFRACTION8A90 - 103
9X-RAY DIFFRACTION9A104 - 114
10X-RAY DIFFRACTION10A115 - 127
11X-RAY DIFFRACTION11A128 - 162
12X-RAY DIFFRACTION12A163 - 181
13X-RAY DIFFRACTION13A182 - 193
14X-RAY DIFFRACTION14A194 - 210
15X-RAY DIFFRACTION15A211 - 246
16X-RAY DIFFRACTION16A247 - 261
17X-RAY DIFFRACTION17A262 - 280
18X-RAY DIFFRACTION18A281 - 297
19X-RAY DIFFRACTION19A298 - 304
20X-RAY DIFFRACTION20A305 - 309
21X-RAY DIFFRACTION21B1 - 7
22X-RAY DIFFRACTION22B8 - 49
23X-RAY DIFFRACTION23B50 - 54
24X-RAY DIFFRACTION24B55 - 76
25X-RAY DIFFRACTION25B77 - 86
26X-RAY DIFFRACTION26B87 - 100
27X-RAY DIFFRACTION27B101 - 112
28X-RAY DIFFRACTION28B113 - 127
29X-RAY DIFFRACTION29B128 - 140
30X-RAY DIFFRACTION30B141 - 181
31X-RAY DIFFRACTION31B182 - 193
32X-RAY DIFFRACTION32B194 - 207
33X-RAY DIFFRACTION33B208 - 216
34X-RAY DIFFRACTION34B217 - 235
35X-RAY DIFFRACTION35B236 - 248
36X-RAY DIFFRACTION36B249 - 261
37X-RAY DIFFRACTION37B262 - 280
38X-RAY DIFFRACTION38B281 - 297
39X-RAY DIFFRACTION39B298 - 305
40X-RAY DIFFRACTION40B306 - 310

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