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- PDB-3x27: Structure of McbB in complex with tryptophan -

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Basic information

Entry
Database: PDB / ID: 3x27
TitleStructure of McbB in complex with tryptophan
ComponentsCucumopine synthase
KeywordsLYASE / McbB / Pictet-Spenglerase
Function / homologyCyclophilin - #20 / Cucumopine synthase, C-terminal helical bundle domain / Cucumopine synthase C-terminal helical bundle domain / Cyclophilin / Beta Barrel / Mainly Beta / TRYPTOPHAN / Cucumopine synthase
Function and homology information
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.481 Å
AuthorsMori, T. / Sahashi, S. / Morita, H. / Abe, I.
CitationJournal: Chem.Biol. / Year: 2015
Title: Structural Basis for beta-Carboline Alkaloid Production by the Microbial Homodimeric Enzyme McbB
Authors: Mori, T. / Hoshino, S. / Sahashi, S. / Wakimoto, T. / Matsui, T. / Morita, H. / Abe, I.
History
DepositionDec 10, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Other
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Cucumopine synthase
B: Cucumopine synthase
C: Cucumopine synthase
D: Cucumopine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,6328
Polymers153,8154
Non-polymers8174
Water9,566531
1
A: Cucumopine synthase
B: Cucumopine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3164
Polymers76,9082
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-52 kcal/mol
Surface area22330 Å2
MethodPISA
2
C: Cucumopine synthase
D: Cucumopine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3164
Polymers76,9082
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-49 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.760, 108.810, 146.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cucumopine synthase


Mass: 38453.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinactinospora thermotolerans (bacteria)
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: R4QPW9
#2: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM Tris-HCl, 18% PEG1000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 17, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 56928 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.088
Reflection shellResolution: 2.48→2.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.399 / % possible all: 98.5

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Processing

Software
NameVersionClassification
XDSdata scaling
AutoSolphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.481→47.764 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 22.25 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2361 2847 5 %
Rwork0.1772 --
obs0.1802 56923 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.481→47.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10035 0 60 531 10626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810380
X-RAY DIFFRACTIONf_angle_d1.13314201
X-RAY DIFFRACTIONf_dihedral_angle_d13.4783767
X-RAY DIFFRACTIONf_chiral_restr0.0771577
X-RAY DIFFRACTIONf_plane_restr0.0051823
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4812-2.5240.27571360.2041258096
2.524-2.56990.26471400.1932661100
2.5699-2.61930.26251400.19632660100
2.6193-2.67280.26061410.18592684100
2.6728-2.73090.28891410.19162681100
2.7309-2.79440.27751410.19832679100
2.7944-2.86430.25871420.20212682100
2.8643-2.94170.25071420.19682695100
2.9417-3.02830.31211400.20362675100
3.0283-3.1260.27581420.2012685100
3.126-3.23770.28451400.19852671100
3.2377-3.36730.25461430.18982706100
3.3673-3.52050.24861420.18872707100
3.5205-3.70610.25761430.18572716100
3.7061-3.93810.22581420.16882701100
3.9381-4.2420.1971440.14842723100
4.242-4.66860.20261440.14012736100
4.6686-5.34340.17881440.14552741100
5.3434-6.72910.21921470.18712799100
6.7291-47.77270.19061530.16422894100

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