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- PDB-4s23: Structure of the GcpE-HMBPP complex from Thermus thermophilius -

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Basic information

Entry
Database: PDB / ID: 4s23
TitleStructure of the GcpE-HMBPP complex from Thermus thermophilius
Components4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
KeywordsOXIDOREDUCTASE / TIM barrel / alpha/beta fold
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) / 4-hydroxy-3-methylbut-2-enyl-diphosphate synthase activity (flavodoxin) / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / 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 / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / 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 / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Dihydropteroate synthase-like / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-H6P / IRON/SULFUR CLUSTER / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) / 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: 1.65 Å
AuthorsRekittke, I. / Warkentin, E. / Jomaa, H. / Ermler, E.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Structure of the GcpE-HMBPP complex from Thermus thermophilius.
Authors: Rekittke, I. / Warkentin, E. / Jomaa, H. / Ermler, U.
History
DepositionJan 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_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_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_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_asym_id / _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_asym_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
B: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1808
Polymers88,5622
Non-polymers1,6186
Water39,9212216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-61 kcal/mol
Surface area30780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.250, 63.250, 372.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: ispG, gcpE / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli)
References: UniProt: Q84GJ3, UniProt: Q5SLI8*PLUS, EC: 1.17.7.1
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: 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
#4: Chemical ChemComp-H6P / (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate


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


Mass: 18.015 Da / Num. of mol.: 2216 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.6 L enzyme solution, containing 5 mM HMBPP, and 0.6 L precipitant composed of 45% pentaerythritol propoxylate 426, 0.1 M MES pH 6.0, 0.4 M KCl, 0.1% NaN3 (JBScreen Pentaerythritol 1, C6, ...Details: 0.6 L enzyme solution, containing 5 mM HMBPP, and 0.6 L precipitant composed of 45% pentaerythritol propoxylate 426, 0.1 M MES pH 6.0, 0.4 M KCl, 0.1% NaN3 (JBScreen Pentaerythritol 1, C6, Jena Bioscience) and 0.1 L; random microseeding, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.972 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.65→62 Å / Num. all: 95074 / Num. obs: 95074 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.09 / Rsym value: 0.089 / Net I/σ(I): 16.7
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.3 / % possible all: 73.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GcpE-MEcPP, PDB entry 4g9p

4g9p


Resolution: 1.65→19.946 Å / σ(F): 1.37 / Phase error: 15.17 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1701 4903 5.17 %
Rwork0.1202 --
obs0.128 94899 94.43 %
all-94961 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→19.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6200 0 70 2216 8486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086438
X-RAY DIFFRACTIONf_angle_d1.3248749
X-RAY DIFFRACTIONf_dihedral_angle_d14.4212497
X-RAY DIFFRACTIONf_chiral_restr0.048996
X-RAY DIFFRACTIONf_plane_restr0.0061135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6503-1.67880.29891680.20983039X-RAY DIFFRACTION60
1.6788-1.70930.28581770.20393569X-RAY DIFFRACTION70
1.7093-1.74210.26832000.19613853X-RAY DIFFRACTION78
1.7421-1.77770.25032270.18824108X-RAY DIFFRACTION83
1.7777-1.81630.25662430.18434356X-RAY DIFFRACTION87
1.8163-1.85850.24312370.17264617X-RAY DIFFRACTION91
1.8585-1.90490.22542440.16454594X-RAY DIFFRACTION93
1.9049-1.95640.20252690.16114702X-RAY DIFFRACTION94
1.9564-2.01390.17842370.15164768X-RAY DIFFRACTION95
2.0139-2.07890.18712640.14754741X-RAY DIFFRACTION95
2.0789-2.15310.19162720.13924774X-RAY DIFFRACTION95
2.1531-2.23920.18162700.13494757X-RAY DIFFRACTION95
2.2392-2.34090.17622490.1284788X-RAY DIFFRACTION95
2.3409-2.46410.1652320.1254747X-RAY DIFFRACTION95
2.4641-2.61820.17582440.11754800X-RAY DIFFRACTION95
2.6182-2.81980.15352330.11094761X-RAY DIFFRACTION95
2.8198-3.10250.1542660.10224752X-RAY DIFFRACTION95
3.1025-3.54920.14172640.09454794X-RAY DIFFRACTION95
3.5492-4.46290.13692300.08784791X-RAY DIFFRACTION95
4.4629-19.63950.14392610.10134777X-RAY DIFFRACTION95
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)
10.30460.0044-0.00970.3626-0.17170.29430.00470.0533-0.0088-0.0476-0.00210.00340.01540.0278-0.00240.10560.0085-0.00110.1325-0.02160.023845.28091.166-15.4728
20.473-0.02480.13320.3895-0.00130.47160.0076-0.06220.01860.0396-0.00030.0079-0.01450.0044-0.00730.10410.00290.00250.1101-0.0170.019727.294411.852215.4046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and (resid 2 through 290 )) or (chain 'B' and (resid 291 through 406 ))
2X-RAY DIFFRACTION2(chain 'A' and (resid 291 through 406 )) or (chain 'B' and (resid 2 through 290 ))

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