HEADER CHEMOKINE 19-MAY-99 1CM9 TITLE CRYSTAL STRUCTURE OF VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (VIRAL MACROPHAGE INFLAMMATORY PROTEIN-II); COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: VMIP-II; COMPND 5 OTHER_DETAILS: SYNTHETIC SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 8; SOURCE 3 ORGANISM_TAXID: 37296; SOURCE 4 OTHER_DETAILS: NON-BIOLOGICAL SEQUENCE KEYWDS CHEMOKINE, HERPESVIRUS-8, KARPOSI'S SARCOMA EXPDTA X-RAY DIFFRACTION AUTHOR E.J.FERNANDEZ,E.LOLIS REVDAT 7 20-NOV-24 1CM9 1 REMARK REVDAT 6 27-DEC-23 1CM9 1 LINK REVDAT 5 16-NOV-11 1CM9 1 VERSN HETATM REVDAT 4 24-FEB-09 1CM9 1 VERSN REVDAT 3 09-MAY-06 1CM9 1 REMARK REVDAT 2 21-FEB-01 1CM9 1 COMPND JRNL REMARK REVDAT 1 24-JUN-99 1CM9 0 JRNL AUTH E.J.FERNANDEZ,J.WILKEN,D.A.THOMPSON,S.C.PEIPER,E.LOLIS JRNL TITL COMPARISON OF THE STRUCTURE OF VMIP-II WITH EOTAXIN-1, JRNL TITL 2 RANTES, AND MCP-3 SUGGESTS A UNIQUE MECHANISM FOR CCR3 JRNL TITL 3 ACTIVATION. JRNL REF BIOCHEMISTRY V. 39 12837 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 11041848 JRNL DOI 10.1021/BI001166F REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 7859 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 833 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1042 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 22 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.311 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000001085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-98 REMARK 200 TEMPERATURE (KELVIN) : 123 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793, 0.9790, 0.9871 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8259 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.12500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.80500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.12500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.80500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 81 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 ASP A 2 REMARK 465 THR A 3 REMARK 465 LEU A 4 REMARK 465 GLY A 5 REMARK 465 ALA A 6 REMARK 465 GLY B 1 REMARK 465 ASP B 2 REMARK 465 THR B 3 REMARK 465 LEU B 4 REMARK 465 GLY B 5 REMARK 465 ALA B 6 REMARK 465 SER B 7 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 7 OG REMARK 470 TRP A 8 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 8 CZ3 CH2 REMARK 470 ARG A 10 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 12 CG OD1 OD2 REMARK 470 ARG A 74 CG CD NE CZ NH1 NH2 REMARK 470 TRP B 8 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 8 CZ3 CH2 REMARK 470 LYS B 20 CG CD CE NZ REMARK 470 ARG B 21 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 51 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 74 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLN A 19 NE ARG A 21 1.87 REMARK 500 O LEU A 69 O HOH A 77 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TRP A 8 92.07 -39.19 REMARK 500 ARG A 10 144.04 -21.77 REMARK 500 SER A 30 -165.31 -164.33 REMARK 500 SER B 30 -175.60 -170.70 REMARK 500 LYS B 57 6.46 -69.68 REMARK 500 REMARK 500 REMARK: NULL DBREF 1CM9 A 1 74 UNP Q98157 VMI2_HHV8 21 94 DBREF 1CM9 B 1 74 UNP Q98157 VMI2_HHV8 21 94 SEQRES 1 A 74 GLY ASP THR LEU GLY ALA SER TRP HIS ARG PRO ASP LYS SEQRES 2 A 74 CYS CYS LEU GLY TYR GLN LYS ARG PRO LEU PRO GLN VAL SEQRES 3 A 74 LEU LEU SER SER TRP TYR PRO THR SER GLN LEU CYS SER SEQRES 4 A 74 LYS PRO GLY VAL ILE PHE LEU THR LYS ARG GLY ARG GLN SEQRES 5 A 74 VAL CYS ALA ASP LYS SER LYS ASP TRP VAL LYS LYS LEU SEQRES 6 A 74 MSE GLN GLN LEU PRO VAL THR ALA ARG SEQRES 1 B 74 GLY ASP THR LEU GLY ALA SER TRP HIS ARG PRO ASP LYS SEQRES 2 B 74 CYS CYS LEU GLY TYR GLN LYS ARG PRO LEU PRO GLN VAL SEQRES 3 B 74 LEU LEU SER SER TRP TYR PRO THR SER GLN LEU CYS SER SEQRES 4 B 74 LYS PRO GLY VAL ILE PHE LEU THR LYS ARG GLY ARG GLN SEQRES 5 B 74 VAL CYS ALA ASP LYS SER LYS ASP TRP VAL LYS LYS LEU SEQRES 6 B 74 MSE GLN GLN LEU PRO VAL THR ALA ARG MODRES 1CM9 MSE A 66 MET SELENOMETHIONINE MODRES 1CM9 MSE B 66 MET SELENOMETHIONINE HET MSE A 66 8 HET MSE B 66 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 HOH *22(H2 O) HELIX 1 1 GLN A 25 LEU A 27 5 3 HELIX 2 2 ASP A 60 GLN A 68 1 9 HELIX 3 3 GLN B 25 LEU B 27 5 3 HELIX 4 4 ASP B 60 GLN B 68 1 9 SHEET 1 A 3 GLN A 52 ALA A 55 0 SHEET 2 A 3 VAL A 43 THR A 47 -1 N PHE A 45 O VAL A 53 SHEET 3 A 3 LEU A 28 PRO A 33 -1 N TYR A 32 O ILE A 44 SHEET 1 B 3 GLN B 52 ALA B 55 0 SHEET 2 B 3 VAL B 43 THR B 47 -1 N PHE B 45 O VAL B 53 SHEET 3 B 3 LEU B 28 PRO B 33 -1 N TYR B 32 O ILE B 44 SSBOND 1 CYS A 14 CYS A 38 1555 1555 2.05 SSBOND 2 CYS A 15 CYS A 54 1555 1555 2.04 SSBOND 3 CYS B 14 CYS B 38 1555 1555 2.04 SSBOND 4 CYS B 15 CYS B 54 1555 1555 2.05 LINK C LEU A 65 N MSE A 66 1555 1555 1.33 LINK C MSE A 66 N GLN A 67 1555 1555 1.33 LINK C LEU B 65 N MSE B 66 1555 1555 1.33 LINK C MSE B 66 N GLN B 67 1555 1555 1.33 CRYST1 70.250 57.610 49.560 90.00 130.85 90.00 C 1 2 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014235 0.000000 0.012309 0.00000 SCALE2 0.000000 0.017358 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026675 0.00000