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- PDB-2mcm: MACROMOMYCIN -

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Basic information

Entry
Database: PDB / ID: 2mcm
TitleMACROMOMYCIN
ComponentsMACROMOMYCIN
KeywordsAPOPROTEIN
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 macromomyceticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsVan Roey, P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 1989
Title: Crystal structure analysis of auromomycin apoprotein (macromomycin) shows importance of protein side chains to chromophore binding selectivity.
Authors: Van Roey, P. / Beerman, T.A.
History
DepositionMay 8, 1991Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Category: pdbx_database_status / struct_conf / Item: _pdbx_database_status.process_site
Remark 700SHEET THE STRUCTURE CONSISTS OF A SEVEN-STRANDED ANTIPARALLEL BETA-BARREL (FLATTENED) AND TWO ...SHEET THE STRUCTURE CONSISTS OF A SEVEN-STRANDED ANTIPARALLEL BETA-BARREL (FLATTENED) AND TWO ANTIPARALLEL BETA-RIBBONS. THE FOLDING OF THE BETA-BARREL HAS SIMILAR GREEK KEY MOTIF AS THE C DOMAIN OF IMMUNOGLOBULIN. THE STRUCTURE IS COMPOSED OF A FLATTENED SEVEN-STRANDED ANTIPARALLEL BETA-BARREL AND TWO ANTIPARALLEL BETA-SHEET RIBBONS. THE BARREL AND RIBBONS DEFINE A DEEP CLEFT THAT IS THE CHROMOPHORE BINDING SITE. RESIDUES LISTED UNDER SITE REFER TO RESIDUES THAT HAVE SIDE CHAINS EXTENDING INTO THIS AREA. THE SHEET PRESENTED AS *BRL* ON SHEET RECORDS BELOW IS ACTUALLY A SEVEN-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A EIGHT-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MACROMOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1505
Polymers10,7561
Non-polymers3954
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.290, 35.580, 38.040
Angle α, β, γ (deg.)90.00, 99.59, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUE PRO 8 IS A CIS PROLINE.

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Components

#1: Protein MACROMOMYCIN


Mass: 10755.872 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces macromomyceticus (bacteria)
References: UniProt: P01549
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CHROMOPHORE BINDING SITE IS LOCATED BETWEEN THE BARREL AND THE RIBBONS. RESIDUES LISTED ON SITE ...THE CHROMOPHORE BINDING SITE IS LOCATED BETWEEN THE BARREL AND THE RIBBONS. RESIDUES LISTED ON SITE CHR RECORDS ARE THOSE THAT HAVE SIDE CHAINS EXTENDING INTO THIS AREA.
Nonpolymer detailsTHE CALCIUM COORDINATION IS A DISTORTED PENTAGONAL BIPYRAMID. LIGANDS COME FROM THREE DIFFERENT ...THE CALCIUM COORDINATION IS A DISTORTED PENTAGONAL BIPYRAMID. LIGANDS COME FROM THREE DIFFERENT PROTEIN MOLECULES AN TWO WATER MOLECULES. O LEU 89 AND OD1 ASP 79 ARE THE TOP AND BOTTOM OF THE BIPYRAMID. ONE LIGAND IN THE PENTAGON IS MISSING. THIS AREA IS EXPOSED TO THE LESS ORDERED SOLVENT. A WATER MOLECULE (HOH 209) IS PRESENT IN APPROXIMATELY THE RIGHT ORIENTATION BUT 3.23 ANGSTROMS FROM THE CALCIUM. BECAUSE OF PDB FORMAT DEFINITIONS THE LIGANDS THE CALCIUM THAT ARE IN DIFFERENT PROTEIN MOLECULES CANNOT BE PRESENTED ON CONECT RECORDS BELOW. THEY ARE: O LEU 89 (-X, Y + 1/2, -Z) OD1 ASP 79 (-X, Y - 1/2, -Z)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal
*PLUS
Density % sol: 44 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
225 mMTris-HCl1drop
35 mM1dropCaCl2
435 %(w/v)MPD1droppH8.0
568 %(w/v)MPD1reservoir
625 mMTris-HCl1reservoirpH8.0

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.5→10 Å / σ(F): 2
Details: A NUMBER OF WATERS ARE DISORDERED AND ARE PRESENTED IN TWO OR MORE ALTERNATE CONFORMATIONS. BECAUSE OF THE REFINEMENT PROCEDURE USED, THE OCCUPANCIES DO NOT ADD UP TO 1.0 FOR WATERS IN ALTERNATE CONFORMATIONS.
RfactorNum. reflection
obs0.153 13119
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 25 109 886
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0360.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0580.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.461.5
X-RAY DIFFRACTIONp_mcangle_it2.191.5
X-RAY DIFFRACTIONp_scbond_it1.761.5
X-RAY DIFFRACTIONp_scangle_it2.762
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.220.15
X-RAY DIFFRACTIONp_singtor_nbd0.1770.5
X-RAY DIFFRACTIONp_multtor_nbd0.2140.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2210.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor32.5
X-RAY DIFFRACTIONp_staggered_tor11.615
X-RAY DIFFRACTIONp_orthonormal_tor12.215
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.179 / Highest resolution: 1.6 Å / Lowest resolution: 8 Å / Num. reflection obs: 12674
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.024
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.6
X-RAY DIFFRACTIONp_mcbond_it1.46
X-RAY DIFFRACTIONp_scbond_it1.76
X-RAY DIFFRACTIONp_mcangle_it2.19
X-RAY DIFFRACTIONp_scangle_it2.76

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