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- PDB-3t0g: IspH:HMBPP (substrate) structure of the T167C mutant -

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Basic information

Entry
Database: PDB / ID: 3t0g
TitleIspH:HMBPP (substrate) structure of the T167C mutant
Components4-hydroxy-3-methylbut-2-enyl diphosphate reductase
KeywordsOXIDOREDUCTASE / 3Fe-4S iron-sulfur cluster / conserved cysteine / IPP and DMAPP production final step / non-mevalonate pathway / substrate HMBPP / low activity
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-en-1-yl 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 / Chem-H6P / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSpan, I. / Graewert, T. / Bacher, A. / Eisenreich, W. / Groll, M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structures of Mutant IspH Proteins Reveal a Rotation of the Substrate's Hydroxymethyl Group during Catalysis.
Authors: Span, I. / Grawert, T. / Bacher, A. / Eisenreich, W. / Groll, M.
History
DepositionJul 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Sep 13, 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_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 / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)73,5666
Polymers72,4502
Non-polymers1,1164
Water2,540141
1
A: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7833
Polymers36,2251
Non-polymers5582
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)36,7833
Polymers36,2251
Non-polymers5582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.540, 80.850, 112.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 1 - 309 / Label seq-ID: 13 - 321

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 36225.070 Da / Num. of mol.: 2 / Mutation: T167C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ispH, lytB, yaaE, b0029, JW0027 / Production host: Escherichia coli (E. coli)
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-H6P / (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate / (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate


Mass: 262.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O8P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM lithium sulfate, 25% PEG3350, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING 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: Apr 11, 2011
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 37749 / Num. obs: 37485 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 9.1
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.8 / % possible all: 97.2

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F7T

3f7t


Resolution: 2.1→10 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 13.661 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27753 1855 5 %RANDOM
Rwork0.21487 ---
obs0.21801 35246 100 %-
all-37101 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.758 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2---3.28 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4771 0 44 141 4956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224894
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.9756631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.68124.159226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58815854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4671544
X-RAY DIFFRACTIONr_chiral_restr0.1260.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213674
X-RAY DIFFRACTIONr_mcbond_it0.9681.53079
X-RAY DIFFRACTIONr_mcangle_it1.66524968
X-RAY DIFFRACTIONr_scbond_it2.84531815
X-RAY DIFFRACTIONr_scangle_it4.3314.51651
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2389 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.390.5
Amedium thermal1.222
Bmedium positional0.390.5
Bmedium thermal1.222
LS refinement shellResolution: 2.1→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 127 -
Rwork0.282 2399 -
obs--100 %
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)
10.6007-0.87450.00341.71630.55660.71770.0356-0.09910.21530.06660.0958-0.40780.1574-0.0563-0.13150.0418-0.0131-0.00630.0374-0.01820.1102-8.9788-7.9518-7.4654
20.1462-0.2289-0.00890.43890.00010.00310.0517-0.017-0.0085-0.1021-0.0527-0.0022-0.00060.01310.0010.02610.0086-0.00310.08320.00310.0227-29.6165-10.1267-10.614
31.65340.63291.10325.66740.98240.79980.25790.0364-0.1352-0.2477-0.21940.23410.1131-0.0005-0.03850.10650.0173-0.07140.0344-0.02040.0513-40.2438-13.4406-21.5898
44.2813-1.2586-0.23741.2952-0.95341.14750.23070.2305-0.3297-0.1308-0.19870.14370.04790.1419-0.03210.05890.0078-0.00870.0528-0.02680.0313-26.7017-10.435-21.5539
55.6626-2.0861.7824.57830.99961.5440.23660.9909-0.0212-0.5829-0.2475-0.1627-0.06860.31510.01090.11380.02040.03820.1881-0.02790.0412-37.484-9.9984-27.4885
60.0634-0.1628-0.16072.31870.18490.48710.06270.0504-0.002-0.1275-0.06570.2436-0.0282-0.1350.0030.13050.03460.00110.0857-0.00940.0341-41.1832-4.6925-20.6953
71.39110.6235-0.4473.91852.86663.06550.02890.07970.2472-0.125-0.21430.55040.079-0.2580.18540.12830.0115-0.07610.0907-0.00160.1338-48.5854-0.4793-22.3764
80.23470.0738-0.19281.2321-0.12120.16160.06110.0061-0.0062-0.108-0.06050.0554-0.046-0.0045-0.00050.03090.0105-0.00780.0591-0.0080.0146-38.804-0.4756-11.5937
96.96532.62190.57814.0092.43842.2320.2744-0.24170.22920.6111-0.18110.32260.2148-0.267-0.09340.15590.03770.13730.08330.0560.2146-43.642515.5043-9.089
100.3217-0.8942-0.66346.52561.80391.3688-0.0174-0.00650.0322-0.23930.08880.18270.03390.0157-0.07140.02630.0121-0.01760.04710.01160.0227-30.954211.767-17.7106
112.06120.88780.32612.12850.00240.7357-0.14140.1290.1523-0.21060.12760.2569-0.0478-0.01690.01380.0344-0.0003-0.0170.02970.03060.0426-34.421820.8701-16.4872
120.2663-0.72580.23872.1431-0.69330.2256-0.0165-0.003-0.00410.05880.0065-0.0294-0.0150.00080.010.02950.01030.01630.0365-0.00130.0252-23.600614.2227-10.3343
131.76861.6123-0.79082.7691-3.16915.04030.0654-0.02440.11170.2227-0.0020.1048-0.2612-0.038-0.06350.0865-0.00340.01260.0136-0.01480.0211-29.29322.5851-5.3559
141.5837-0.44590.00530.3468-0.19930.18010.057-0.10210.0904-0.0628-0.01280.01640.03730.0228-0.04420.03150.00720.00440.0517-0.00640.0183-19.26142.7764-6.0288
150.49980.125-0.19160.67420.22010.18630.00770.04090.0159-0.00870.0115-0.0485-0.001-0.0165-0.01920.01820.00350.0210.03620.00620.0272-11.45950.1612-16.113
162.6761-0.0467-0.23230.041-0.04035.1328-0.06960.1572-0.0261-0.05220.004-0.06710.10240.30590.06560.0732-0.0090.09050.0309-0.01140.1141-2.7758-8.6424-21.0433
171.6050.29520.08922.0070.04820.00560.0441-0.0798-0.10870.0667-0.036-0.00310.0031-0.0068-0.00810.03150.01220.0090.03520.00780.0128-14.7064-12.0026-13.7944
182.6871-1.3116-2.55421.54132.20714.26760.0364-0.1859-0.1550.11590.0163-0.17630.12330.0756-0.05270.0304-0.0027-0.0350.03260.03350.0859-7.6419-11.9865-7.7052
195.05631.70672.71030.63761.11042.11820.0816-0.0893-0.14120.0589-0.0467-0.04950.1689-0.1265-0.03490.0326-0.01250.020.0383-0.00570.0452-31.2907-7.3296-1.8958
204.84-2.4158-2.04648.03922.58866.97460.0408-0.0336-0.0680.39820.02690.3130.1265-0.4087-0.06760.0271-0.00270.01360.040.00540.0252-44.01-13.5126-7.5579
211.12740.13270.50640.5646-0.2510.644-0.0710.1152-0.062-0.12740.11290.1350.0609-0.0535-0.04190.0418-0.0228-0.02720.0541-0.00350.0647-56.5756-7.53088.2066
220.5397-0.31410.39910.445-0.24770.41390.01130.0574-0.00110.05020.0277-0.0190.0409-0.0028-0.03910.03880.0002-0.02310.03710.00950.0177-33.3292-10.928617.987
233.52080.8954-0.29775.49520.58750.88910.2467-0.1124-0.11770.1109-0.1565-0.23350.0948-0.1844-0.09020.0332-0.034-0.02050.04720.02560.0189-33.1718-17.549425.7322
241.06050.04620.27780.3883-0.29780.32440.0476-0.00970.0017-0.0342-0.00590.04420.0430.0133-0.04170.03520.006-0.02290.0601-0.02180.0223-24.3715-5.433524.7875
252.389-0.40082.94081.3252-2.00655.6113-0.06480.07140.2890.0294-0.1427-0.0577-0.05470.22180.20760.0188-0.0087-0.04020.03420.01450.1676-17.81052.272520.8108
261.6941-0.99331.69740.6917-0.83431.94380.05130.0482-0.0146-0.03590.0168-0.02920.03280.0961-0.06810.0433-0.0045-0.02010.048-0.00590.0271-22.7375-4.032115.839
275.78014.16910.37215.6722.30711.58360.18610.31910.3173-0.18010.0634-0.1291-0.2253-0.1109-0.24950.05460.03090.02940.02880.0390.1044-23.174312.40058.772
280.0994-0.554-0.03593.09210.18350.1091-0.0327-0.01280.0290.16480.0796-0.1506-0.0012-0.0606-0.04690.03510.0112-0.02990.04850.01550.0546-32.482313.474816.8976
292.46550.6664-0.0091.5644-0.12771.0290.0044-0.38750.24420.0675-0.0041-0.18080.02020.0643-0.00030.0386-0.0038-0.05930.076-0.04440.133-23.241915.05317.8675
301.46590.6647-0.0291.7778-0.02180.28170.0162-0.03490.16740.11460.0255-0.0633-0.0258-0.0806-0.04170.02140.0084-0.00210.02550.00290.0397-37.539719.962913.4453
311.56391.41431.00416.83613.76312.11260.02810.11180.3958-0.1191-0.15490.109-0.047-0.0620.12680.0789-0.01280.02460.02590.03660.1129-36.050122.60665.4211
322.72211.564-0.70131.1691-0.18120.36390.02280.04250.039-0.0069-0.00940.0191-0.0224-0.0287-0.01330.01870.0037-0.01040.05530.01140.0101-43.82183.26846.2212
338.06070.0847-3.45710.0014-0.03154.09980.09820.04360.3657-0.0005-0.00270.0104-0.1888-0.0447-0.09540.01340.0031-0.01780.0079-0.01070.1121-60.18430.48548.5394
340.7249-0.1345-0.42240.5834-0.60081.0765-0.0679-0.0299-0.0760.18990.04930.0449-0.1741-0.01570.01850.0660.0060.01230.04110.00990.0339-48.91580.589817.6255
350.7992-1.27890.75984.4549-0.4730.96-0.0901-0.068200.22460.04970.1659-0.0624-0.06570.04040.0239-0.00210.02140.0447-0.00880.0333-56.1005-0.669718.815
365.6176-1.93550.92392.8908-0.57695.9344-0.0912-0.4252-0.01810.32990.11120.49320.1581-0.5575-0.020.0491-0.01560.06710.0748-0.00970.107-63.5521-7.810121.7719
371.33070.0949-0.38321.72260.37720.20590.02250.0625-0.03680.09-0.04440.06050.0137-0.02660.02190.0266-0.0103-0.00860.03670.01040.0136-50.5492-11.439114.3489
382.18981.355-2.12524.1304-1.27054.2041-0.00370.2704-0.0438-0.14060.10310.45310.2738-0.2689-0.09940.04010.0014-0.03890.0347-0.01460.0814-57.6718-11.42488.6176
394.4463-1.25142.84850.3777-0.92612.4401-0.02590.1857-0.0215-0.0334-0.0402-0.00990.19040.09890.06610.07340.0010.0240.0684-0.01120.0119-32.9204-7.70923.1076
407.3486-0.5575-1.70451.48670.81882.5149-0.02560.32390.146-0.06160.125-0.14080.18620.157-0.09940.02770.01120.00470.0442-0.00720.0147-22.2258-15.48297.9667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION1A997
3X-RAY DIFFRACTION2A8 - 24
4X-RAY DIFFRACTION3A25 - 37
5X-RAY DIFFRACTION4A38 - 49
6X-RAY DIFFRACTION5A50 - 64
7X-RAY DIFFRACTION6A65 - 77
8X-RAY DIFFRACTION7A78 - 89
9X-RAY DIFFRACTION8A90 - 103
10X-RAY DIFFRACTION9A104 - 114
11X-RAY DIFFRACTION10A115 - 127
12X-RAY DIFFRACTION11A128 - 162
13X-RAY DIFFRACTION12A163 - 181
14X-RAY DIFFRACTION13A182 - 193
15X-RAY DIFFRACTION14A194 - 210
16X-RAY DIFFRACTION15A211 - 246
17X-RAY DIFFRACTION16A247 - 261
18X-RAY DIFFRACTION17A262 - 280
19X-RAY DIFFRACTION18A281 - 297
20X-RAY DIFFRACTION19A298 - 304
21X-RAY DIFFRACTION20A305 - 309
22X-RAY DIFFRACTION21B1 - 7
23X-RAY DIFFRACTION21B997
24X-RAY DIFFRACTION22B8 - 49
25X-RAY DIFFRACTION23B50 - 54
26X-RAY DIFFRACTION24B55 - 76
27X-RAY DIFFRACTION25B77 - 86
28X-RAY DIFFRACTION26B87 - 100
29X-RAY DIFFRACTION27B101 - 112
30X-RAY DIFFRACTION28B113 - 127
31X-RAY DIFFRACTION29B128 - 140
32X-RAY DIFFRACTION30B141 - 181
33X-RAY DIFFRACTION31B182 - 193
34X-RAY DIFFRACTION32B194 - 207
35X-RAY DIFFRACTION33B208 - 216
36X-RAY DIFFRACTION34B217 - 235
37X-RAY DIFFRACTION35B236 - 248
38X-RAY DIFFRACTION36B249 - 261
39X-RAY DIFFRACTION37B262 - 280
40X-RAY DIFFRACTION38B281 - 297
41X-RAY DIFFRACTION39B298 - 305
42X-RAY DIFFRACTION40B306 - 310

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