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- PDB-1ump: GEOMETRY OF TRITERPENE CONVERSION TO PENTACARBOCYCLIC HOPENE -

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Entry
Database: PDB / ID: 1ump
TitleGEOMETRY OF TRITERPENE CONVERSION TO PENTACARBOCYCLIC HOPENE
ComponentsSQUALENE--HOPENE CYCLASE
KeywordsISOMERASE / TRITERPENE CYCLASE / CHOLESTEROL BIOSYNTHESIS / OXIDOSQUALENE CYCLASE / MONOTOPIC MEMBRANE PROTEIN
Function / homology
Function and homology information


squalene-hopanol cyclase / squalene-hopene cyclase / squalene-hopene cyclase activity / triterpenoid biosynthetic process / lipid droplet / lyase activity / plasma membrane
Similarity search - Function
Squalene hopene cyclase / Terpene synthase, conserved site / Terpene synthases signature. / Squalene cyclase, N-terminal / Squalene-hopene cyclase N-terminal domain / Squalene cyclase / Squalene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / Prenyltransferase alpha-alpha toroid domain / Glycosyltransferase - #20 ...Squalene hopene cyclase / Terpene synthase, conserved site / Terpene synthases signature. / Squalene cyclase, N-terminal / Squalene-hopene cyclase N-terminal domain / Squalene cyclase / Squalene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / Prenyltransferase alpha-alpha toroid domain / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
2-AZASQUALENE / Squalene--hopene cyclase
Similarity search - Component
Biological speciesALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsReinert, D.J. / Balliano, G. / Schulz, G.E.
Citation
Journal: Chem.Biol. / Year: 2004
Title: Conversion of Squalene to the Pentacarbocyclic Hopene
Authors: Reinert, D.J. / Balliano, G. / Schulz, G.E.
#1: Journal: Chem.Biol. / Year: 2002
Title: Crystal Structure of a Squalene Cyclase in Complex with the Potential Anticholesteremic Drug Ro48-8071
Authors: Lenhart, A. / Weihofen, W. / Pleschke, A. / Schulz, G.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: The Structure of the Membrane Protein Squalene-Hopene Cyclase at 2.0 A Resolution
Authors: Wendt, K.U. / Lenhart, A. / Schulz, G.E.
#3: Journal: Science / Year: 1997
Title: Structure and Function of a Squalene Cyclase
Authors: Wendt, K.U. / Poralla, K. / Schulz, G.E.
#4: Journal: Protein Sci. / Year: 1997
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of Squalene-Hopene Cyclase from Alicyclobacillus Acidocaldarius
Authors: Wendt, K.U. / Feil, C. / Lenhart, A. / Poralla, K. / Schulz, G.E.
History
DepositionAug 27, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 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 / 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 / _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: SQUALENE--HOPENE CYCLASE
B: SQUALENE--HOPENE CYCLASE
C: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,72311
Polymers214,9503
Non-polymers2,7738
Water21,7981210
1
A: SQUALENE--HOPENE CYCLASE
hetero molecules

B: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,0477
Polymers143,3002
Non-polymers1,7475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+2/31
MethodPQS
2
B: SQUALENE--HOPENE CYCLASE
hetero molecules

A: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,0477
Polymers143,3002
Non-polymers1,7475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-x+y,-z+2/31
MethodPQS
3
C: SQUALENE--HOPENE CYCLASE
hetero molecules

C: SQUALENE--HOPENE CYCLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,3538
Polymers143,3002
Non-polymers2,0536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)139.144, 139.144, 240.699
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.48174, -0.876224, -0.012599), (0.876286, -0.481559, -0.014949), (0.007031, -0.018242, 0.999809)139.94492, -4.8023, 2.45863
2given(-0.532911, 0.84612, -0.009267), (-0.845892, -0.532985, -0.019856), (-0.02174, -0.002743, 0.99976)77.55786, 120.88502, 2.0045
3given(-0.484575, -0.874286, -0.02847), (0.874749, -0.484308, -0.016101), (0.000289, -0.032706, 0.999465)141.24185, -3.81716, -0.64865
DetailsTHE DIMERIC COMPLEX DESCRIBED HERE IS OF THE TYPE A-B', B-A' AND C-C'

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Components

#1: Protein SQUALENE--HOPENE CYCLASE


Mass: 71650.039 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ALICYCLOBACILLUS ACIDOCALDARIUS (bacteria)
Description: THERMOSTABLE, ACIDOPHILIC / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): JM105 / References: UniProt: P33247, squalene-hopene cyclase
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-SQA / 2-AZASQUALENE / (4E,8E,12Z,16Z)-N,N,4,8,13,17,21-HEPTAMETHYLDOCOSA-4,8,12,16,20-PENTAEN-1-AMINE


Mass: 413.722 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H51N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1210 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES CYCLIZATION OF SQUALENE TO HOPENE. KEY ENZYME IN HOPANOID (TRITERPENOID) METABOLISM.

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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: 2.94 Å3/Da / Density % sol: 57.84 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.8
Details: HANGING DROP WITH 5-8 MG/ML PROTEIN,0.3 PERCENT (W/V) N-OCTYL-TETRAOXYETHYLENE, 50 MM SODIUM CITRATE (PH 4.8), 50 MM SODIUM CHLORIDE, 6...16 PERCENT (V/V) PEG-600 AND 1.5 MOLAR EXCESS (IN ...Details: HANGING DROP WITH 5-8 MG/ML PROTEIN,0.3 PERCENT (W/V) N-OCTYL-TETRAOXYETHYLENE, 50 MM SODIUM CITRATE (PH 4.8), 50 MM SODIUM CHLORIDE, 6...16 PERCENT (V/V) PEG-600 AND 1.5 MOLAR EXCESS (IN RESPECT TO PROTEIN) 2-AZASQUALENE IN THE STARTING DROPLET. RESERVOIR CONTAINED 100 MM SODIUM CITRATE (PH 4.8), 100 MM SODIUM CHLORIDE, 6-16 PERCENT (V/V) PEG-600.
Crystal grow
*PLUS
Temperature: 20.5 ℃ / pH: 4.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
113 mg/mlprotein1drop
2100 mMsodium cirtate1reservoirpH4.8
3100 mM1reservoirNaCl
46-16 %(v/v)PEG6001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98005 Å / Relative weight: 1
ReflectionResolution: 2.13→20 Å / Num. obs: 149921 / % possible obs: 99.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.2
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 4.9 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.13 Å / Lowest resolution: 20 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 4.5 % / Num. unique obs: 11956 / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSZ

1gsz


Resolution: 2.13→19.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.875 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3691 2.5 %RANDOM
Rwork0.186 ---
obs0.187 146229 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0.57 Å20 Å2
2---1.14 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.13→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14892 0 195 1210 16297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02115578
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214076
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.95121133
X-RAY DIFFRACTIONr_angle_other_deg0.853332553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69451854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.22121
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217418
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023462
X-RAY DIFFRACTIONr_nbd_refined0.2040.23563
X-RAY DIFFRACTIONr_nbd_other0.2310.216626
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.28405
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.21058
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5191.59222
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.933214772
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.66636356
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6474.56361
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.13→2.19 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 271
Rwork0.246 10621
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)
11.0336-0.8751-0.38883.41180.93281.83560.13970.07180.3375-0.84350.0682-0.7687-0.15840.1956-0.20790.2846-0.01520.19540.06940.0320.319364.814668.255664.2103
20.83680.1433-0.24391.2473-0.31061.51820.00430.0386-0.0098-0.0470.01720.1249-0.2111-0.1165-0.02150.0810.0563-0.05680.0393-0.04130.059948.077618.208565.8836
34.52320.92071.61620.81440.39931.9381-0.16070.66260.1413-0.15490.11260.0834-0.02390.12320.04810.0767-0.0131-0.00750.11960.00090.0619100.155728.326464.6357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 628
2X-RAY DIFFRACTION2B10 - 628
3X-RAY DIFFRACTION3C10 - 628
Refinement
*PLUS
% reflection Rfree: 2.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3

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