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- PDB-2bm9: cmcI-N160 in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 2bm9
TitlecmcI-N160 in complex with SAM
ComponentsCEPHALOSPORIN HYDROXYLASE CMCI
KeywordsPORIN / CEPHAMYCIN BIOSYNTHESIS
Function / homology
Function and homology information


lipid biosynthetic process / methyltransferase activity / metal ion binding
Similarity search - Function
Rhamnosyl O-methyltransferase/Cephalosporin hydroxylase / Rhamnosyl O-methyltransferase/CmcI / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Cephalosporin hydroxylase CmcI / Cephalosporin hydroxylase CmcI
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsOster, L.M. / Lester, D.R. / Terwisscha Van Scheltinga, A. / Svenda, M. / Genereux, C. / Andersson, I.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Insights Into Cephamycin Biosynthesis: The Crystal Structure of Cmci from Streptomyces Clavuligerus
Authors: Oster, L.M. / Lester, D.R. / Terwisscha Van Scheltinga, A. / Svenda, M. / Van Lun, M. / Genereux, C. / Andersson, I.
History
DepositionMar 10, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 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: CEPHALOSPORIN HYDROXYLASE CMCI
B: CEPHALOSPORIN HYDROXYLASE CMCI
C: CEPHALOSPORIN HYDROXYLASE CMCI
D: CEPHALOSPORIN HYDROXYLASE CMCI
E: CEPHALOSPORIN HYDROXYLASE CMCI
F: CEPHALOSPORIN HYDROXYLASE CMCI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,36412
Polymers165,9746
Non-polymers2,3916
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.805, 103.027, 182.024
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
CEPHALOSPORIN HYDROXYLASE CMCI


Mass: 27662.250 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O85726, UniProt: B5GLB3*PLUS
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 10 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASP 160 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, LEU 10 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASP 160 TO ASN ENGINEERED RESIDUE IN CHAIN A, LEU 200 TO PHE ENGINEERED RESIDUE IN CHAIN B, LEU 10 TO GLN ENGINEERED RESIDUE IN CHAIN B, ASP 160 TO ASN ENGINEERED RESIDUE IN CHAIN B, LEU 200 TO PHE ENGINEERED RESIDUE IN CHAIN C, LEU 10 TO GLN ENGINEERED RESIDUE IN CHAIN C, ASP 160 TO ASN ENGINEERED RESIDUE IN CHAIN C, LEU 200 TO PHE ENGINEERED RESIDUE IN CHAIN D, LEU 10 TO GLN ENGINEERED RESIDUE IN CHAIN D, ASP 160 TO ASN ENGINEERED RESIDUE IN CHAIN D, LEU 200 TO PHE ENGINEERED RESIDUE IN CHAIN E, LEU 10 TO GLN ENGINEERED RESIDUE IN CHAIN E, ASP 160 TO ASN ENGINEERED RESIDUE IN CHAIN E, LEU 200 TO PHE ENGINEERED RESIDUE IN CHAIN F, LEU 10 TO GLN ENGINEERED RESIDUE IN CHAIN F, ASP 160 TO ASN ENGINEERED RESIDUE IN CHAIN F, LEU 200 TO PHE

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorDate: Apr 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.9→91.3 Å / Num. obs: 37586 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BM8

2bm8


Resolution: 2.94→55.05 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.835 / SU B: 24.988 / SU ML: 0.437 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.568 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.329 1885 5 %RANDOM
Rwork0.264 ---
obs0.267 35606 98.6 %-
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: 12.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.08 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.94→55.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11442 0 162 167 11771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02111946
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210439
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.95316258
X-RAY DIFFRACTIONr_angle_other_deg0.839324146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91751383
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_restr0.070.21677
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213348
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022631
X-RAY DIFFRACTIONr_nbd_refined0.2130.22737
X-RAY DIFFRACTIONr_nbd_other0.2150.212901
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.27452
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1620.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3741.56969
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.707211215
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.87434977
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5164.55043
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: 2.94→3.01 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.446 106
Rwork0.345 2143
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)
11.1353-0.4070.90221.85020.33992.16970.0595-0.657-0.08950.3516-0.26530.12460.2507-0.0560.20580.56140.0230.16280.27350.07060.5198-6.65640.69171.337
21.9286-0.28780.29282.3856-0.36191.84290.01750.40510.0338-0.1081-0.1180.1228-0.04490.16620.10050.46980.15410.01330.1290.01950.4832-7.16642.46243.548
31.2812-0.2364-0.53472.04340.24681.5999-0.19020.0311-0.1896-0.19630.04290.04170.36760.56660.14730.48080.27480.04850.49630.10660.330321.85941.08329.237
42.221-0.08620.27331.1169-0.94541.4322-0.12860.37590.08720.01190.0664-0.25730.12760.52630.06220.50490.0544-0.04880.8537-0.0810.475941.66456.63273.33
52.0371-0.3674-0.41411.80640.71952.2472-0.23420.0350.15390.06150.24370.11030.0391-0.0288-0.00950.50860.0855-0.0520.57540.05720.30116.41158.78285.081
61.1058-0.08620.68921.9926-0.12531.8232-0.24230.29850.12630.08280.2666-0.2254-0.10981.4676-0.02430.22790.01870.06581.52520.07440.391341.45257.26940.831
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 233
2X-RAY DIFFRACTION2B4 - 234
3X-RAY DIFFRACTION3C3 - 233
4X-RAY DIFFRACTION4D2 - 233
5X-RAY DIFFRACTION5E3 - 233
6X-RAY DIFFRACTION6F3 - 234

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