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- PDB-1nco: STRUCTURE OF THE ANTITUMOR PROTEIN-CHROMOPHORE COMPLEX NEOCARZINO... -

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Basic information

Entry
Database: PDB / ID: 1nco
TitleSTRUCTURE OF THE ANTITUMOR PROTEIN-CHROMOPHORE COMPLEX NEOCARZINOSTATIN
ComponentsHOLO-NEOCARZINOSTATIN
KeywordsANTIBACTERIAL AND ANTITUMOR PROTEIN
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
NEOCARZINOSTATIN-CHROMOPHORE / Neocarzinostatin
Similarity search - Component
Biological speciesStreptomyces carzinostaticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsKim, K.-H. / Kwon, B.-M. / Myers, A.G. / Rees, D.C.
CitationJournal: Science / Year: 1993
Title: Crystal structure of neocarzinostatin, an antitumor protein-chromophore complex.
Authors: Kim, K.H. / Kwon, B.M. / Myers, A.G. / Rees, D.C.
History
DepositionJul 13, 1993-
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HOLO-NEOCARZINOSTATIN
B: HOLO-NEOCARZINOSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9784
Polymers22,2002
Non-polymers7782
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.400, 90.400, 52.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Atom site foot note1: RESIDUES PRO A 9 AND PRO B 9 ARE CIS PROLINES.
DetailsTHE GENERAL NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS BETWEEN TWO MOLECULES IN THE ASYMMETRIC UNIT WAS DETERMINED BY DENSITY CORRELATION STUDIES AND MANUAL MOLECULAR REPLACEMENT WITH MACROMOMYCIN STRUCTURE AS A MODEL. THE MOLECULE PREFIXED WITH "B" IS THE HOLO-NEOCARZINOSTATIN AND THE MOLECULE WITH "A" IS THE APO-NEOCARZINOSTATIN. THE CURRENT MODEL HAS 226 RESIDUES OF MOLECULES A AND B, 1 NEOCARZINOSTATIN-CHROMOPHORE, 1 MPD AND 161 WATER MOLECULES (1773 NON-HYDROGEN ATOMS TOTAL ).

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Components

#1: Protein HOLO-NEOCARZINOSTATIN


Mass: 11100.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces carzinostaticus (bacteria)
References: UniProt: P0A3R9
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CHR / NEOCARZINOSTATIN-CHROMOPHORE / NCS-CHROMOPHORE / Neocarzinostatin


Mass: 659.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H33NO12 / Comment: antitumor, antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
250 mMsodium acetate1drop
370 %MPD1reservoir
450 mMsodium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 23556 / % possible obs: 87.8 % / Num. measured all: 146707 / Rmerge(I) obs: 0.071

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.199 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 48 169 1773
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.84
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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