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- PDB-4g9p: Structure of the GcpE-MEcPP (IspG) complex from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 4g9p
TitleStructure of the GcpE-MEcPP (IspG) complex from Thermus thermophilus
Components4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
KeywordsOXIDOREDUCTASE / isoprenoid biosynthesis / non mevalonate pathway / iron-sulphur-cluster / TIM-barrel / MEcPP
Function / homology
Function and homology information


(E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase (flavodoxin) / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity (ferredoxin) / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial-type / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial / GcpE protein / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Dihydropteroate synthase-like / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel ...4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial-type / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial / GcpE protein / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Dihydropteroate synthase-like / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE / : / IRON/SULFUR CLUSTER / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin)
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRekittke, I. / Jomaa, H. / Ermler, U.
CitationJournal: Febs Lett. / Year: 2012
Title: Structure of the GcpE (IspG)-MEcPP complex from Thermus thermophilus.
Authors: Rekittke, I. / Jomaa, H. / Ermler, U.
History
DepositionJul 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_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_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-en-1-yl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4118
Polymers44,2811
Non-polymers1,1307
Water8,197455
1
A: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
hetero molecules

A: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,82316
Polymers88,5622
Non-polymers2,26014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area11210 Å2
ΔGint-87 kcal/mol
Surface area30320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.650, 63.650, 442.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase / 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase


Mass: 44281.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: gcpE, ispG, TT_C1677 / Plasmid: PQETTGCPE / Production host: Escherichia coli (E. coli) / References: UniProt: Q72H18, EC: 1.17.7.1

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Non-polymers , 6 types, 462 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-CDI / 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE


Mass: 278.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O9P2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 45 % pentaerythriol propoxylate 426, 0.1 M MES, 0.4 M KCl, 2.5 mM MEcPP, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 77534 / Num. obs: 79313 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.49 / % possible all: 85.4

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→46.782 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 17.27 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2025 3870 5 %
Rwork0.1767 --
obs0.1779 77355 97.83 %
all-77355 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.87 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0573 Å20 Å20 Å2
2--1.0573 Å20 Å2
3----2.1145 Å2
Refinement stepCycle: LAST / Resolution: 1.55→46.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 51 455 3606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123269
X-RAY DIFFRACTIONf_angle_d1.7914451
X-RAY DIFFRACTIONf_dihedral_angle_d13.6591280
X-RAY DIFFRACTIONf_chiral_restr0.072499
X-RAY DIFFRACTIONf_plane_restr0.007575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.56890.34261310.30042099X-RAY DIFFRACTION83
1.5689-1.58880.36191190.29142310X-RAY DIFFRACTION87
1.5888-1.60970.29651080.27062306X-RAY DIFFRACTION89
1.6097-1.63170.24771260.23872454X-RAY DIFFRACTION92
1.6317-1.6550.26471190.23322437X-RAY DIFFRACTION94
1.655-1.67970.25641340.21812582X-RAY DIFFRACTION97
1.6797-1.7060.26551190.19982554X-RAY DIFFRACTION98
1.706-1.7340.20591230.18982638X-RAY DIFFRACTION99
1.734-1.76390.21671270.18642630X-RAY DIFFRACTION100
1.7639-1.79590.21581390.18942602X-RAY DIFFRACTION100
1.7959-1.83050.22961200.17892688X-RAY DIFFRACTION100
1.8305-1.86780.23491390.18832667X-RAY DIFFRACTION100
1.8678-1.90850.22371370.17742615X-RAY DIFFRACTION100
1.9085-1.95290.20861380.17912626X-RAY DIFFRACTION100
1.9529-2.00170.20571630.17792667X-RAY DIFFRACTION100
2.0017-2.05580.21941410.17482663X-RAY DIFFRACTION100
2.0558-2.11630.2031480.17462655X-RAY DIFFRACTION100
2.1163-2.18460.19061490.1752652X-RAY DIFFRACTION100
2.1846-2.26270.22731380.1732668X-RAY DIFFRACTION100
2.2627-2.35330.17121670.16212667X-RAY DIFFRACTION100
2.3533-2.46040.19561530.1672668X-RAY DIFFRACTION100
2.4604-2.59010.1921400.16942693X-RAY DIFFRACTION100
2.5901-2.75240.20021480.16912738X-RAY DIFFRACTION100
2.7524-2.96480.21331520.17012697X-RAY DIFFRACTION100
2.9648-3.26310.20561420.1792764X-RAY DIFFRACTION100
3.2631-3.73510.18511340.16182815X-RAY DIFFRACTION100
3.7351-4.70520.16521560.14512827X-RAY DIFFRACTION100
4.7052-46.80340.18441600.18753103X-RAY DIFFRACTION100
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)
13.0889-0.4250.73771.0015-0.36910.9172-0.04310.12710.0568-0.05980.03860.0449-0.31280.0686-0.04630.2267-0.0184-0.01290.05-0.00650.1104-5.615320.63054.6609
20.7414-0.0039-0.07470.66430.23970.6856-0.0014-0.09690.34370.19110.015-0.0238-0.42850.121-0.0110.3701-0.0336-0.00980.0378-0.0540.1528-3.511425.887816.8765
31.10140.1975-0.30021.9437-0.59641.1201-0.0717-0.32850.17950.27420.17170.3269-0.2565-0.3375-0.03890.24940.06170.03770.2246-0.02460.1716-20.031214.741423.9266
40.33450.08940.08390.36980.09690.8013-0.0139-0.06810.05420.02150.01530.0802-0.1092-0.0886-0.01290.1410.0162-0.00070.0606-0.00080.1159-12.42058.15536.186
50.9396-0.16710.0943.07220.07720.7905-0.0218-0.04160.23750.01520.0359-0.1939-0.23220.13880.01130.1705-0.05060.01160.1221-0.00650.1371.27575.764-19.1707
63.7024-0.7755-0.02795.85080.14552.6373-0.01020.20090.1294-0.1309-0.048-0.2868-0.20170.23450.0420.1815-0.05420.02890.16670.02630.09941.61645.2961-28.5693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:50)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 51:119)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 120:169)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 170:304)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 305:359)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 360:406)

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