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- PDB-2cbm: Crystal structure of the apo-form of a neocarzinostatin mutant ev... -

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Basic information

Entry
Database: PDB / ID: 2cbm
TitleCrystal structure of the apo-form of a neocarzinostatin mutant evolved to bind testosterone.
ComponentsNEOCARZINOSTATIN
KeywordsANTIMICROBIAL / ANTIBIOTIC / DNA-BINDING / PHAGE-DISPLAY
Function / homology
Function and homology information


defense response to bacterium / DNA binding
Similarity search - Function
Neocarzinostatin-like / Neocarzinostatin family / Neocarzinostatin family / Neocarzinostatin-like / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSTREPTOMYCES CARZINOSTATICUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsDrevelle, A. / Graille, M. / Heyd, B. / Sorel, I. / Ulryck, N. / Pecorari, F. / Desmadril, M. / Van Tilbeurgh, H. / Minard, P.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Structures of in Vitro Evolved Binding Sites on Neocarzinostatin Scaffold Reveal Unanticipated Evolutionary Pathways.
Authors: Drevelle, A. / Graille, M. / Heyd, B. / Sorel, I. / Ulryck, N. / Pecorari, F. / Desmadril, M. / Van Tilbeurgh, H. / Minard, P.
#1: Journal: Biochemistry / Year: 2003
Title: In Vitro Evolution of the Binding Specificity of Neocarzinostatin, an Enediyne-Binding Chromoprotein.
Authors: Heyd, B. / Pecorari, F. / Collinet, B. / Adjadj, E. / Desmadril, M. / Minard, P.
History
DepositionJan 6, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEOCARZINOSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4202
Polymers11,2251
Non-polymers1951
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.125, 60.125, 97.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2029-

HOH

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Components

#1: Protein NEOCARZINOSTATIN / NCS / MITOMALCIN / MMC


Mass: 11225.162 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-146 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CARZINOSTATICUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR(DE3) PLYSS / References: UniProt: P0A3R9
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHAS ANTIBIOTIC ACTIVITY FOR GRAM-POSITIVE BACTERIA AND ANTITUMOR ACTIVITY FOR CERTAIN MOUSE TUMORS. ...HAS ANTIBIOTIC ACTIVITY FOR GRAM-POSITIVE BACTERIA AND ANTITUMOR ACTIVITY FOR CERTAIN MOUSE TUMORS. ENGINEERED RESIDUE IN CHAIN A, ASP 67 TO TRP ENGINEERED RESIDUE IN CHAIN A, GLY 69 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 71 TO TRP ENGINEERED RESIDUE IN CHAIN A, TRP 73 TO ARG ENGINEERED RESIDUE IN CHAIN A, LEU 79 TO TRP ENGINEERED RESIDUE IN CHAIN A, CYS 81 TO TYR ENGINEERED RESIDUE IN CHAIN A, PHE 86 TO ASN
Sequence detailsD33W,G35A,C37W,W39R,L45W,C47Y,F52N

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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: 2.11 Å3/Da / Density % sol: 41.3 %
Crystal growDetails: 1.8 M (NH4)2SO4; 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→30 Å / Num. obs: 7137 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 9.38 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 26
Reflection shellResolution: 2.03→2.09 Å / Redundancy: 3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 8.4 / % possible all: 89.5

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NCO

1nco


Resolution: 2.03→30 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 383 5.3 %RANDOM
Rwork0.2182 ---
obs0.2182 6983 97.3 %-
Solvent computationBsol: 45.1893 Å2 / ksol: 0.361113 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-1.521 Å20 Å2
2--0.13 Å20 Å2
3----0.259 Å2
Refinement stepCycle: LAST / Resolution: 2.03→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 0 12 54 856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.223
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3MES.PARAM

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