HEADER ANTI-HIV PROTEIN 07-DEC-98 1B3A TITLE TOTAL CHEMICAL SYNTHESIS AND HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE TITLE 2 POTENT ANTI-HIV PROTEIN AOP-RANTES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (RANTES); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: OXIME LINK BETWEEN AOP GROUP AND PRO3 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS CHEMICAL PROTEIN SYNTHESIS, CHEMOKINE, HIV-1, RANTES, ANTI-HIV KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.WILKEN,D.HOOVER,D.A.THOMPSON,P.N.BARLOW,H.MCSPARRON,L.PICARD, AUTHOR 2 A.WLODAWER,J.LUBKOWSKI,S.B.H.KENT REVDAT 6 30-OCT-24 1B3A 1 REMARK REVDAT 5 27-DEC-23 1B3A 1 REMARK LINK REVDAT 4 04-OCT-17 1B3A 1 REMARK REVDAT 3 24-FEB-09 1B3A 1 VERSN REVDAT 2 01-APR-03 1B3A 1 JRNL REVDAT 1 23-APR-99 1B3A 0 JRNL AUTH J.WILKEN,D.HOOVER,D.A.THOMPSON,P.N.BARLOW,H.MCSPARRON, JRNL AUTH 2 L.PICARD,A.WLODAWER,J.LUBKOWSKI,S.B.KENT JRNL TITL TOTAL CHEMICAL SYNTHESIS AND HIGH-RESOLUTION CRYSTAL JRNL TITL 2 STRUCTURE OF THE POTENT ANTI-HIV PROTEIN AOP-RANTES. JRNL REF CHEM.BIOL. V. 6 43 1999 JRNL REFN ISSN 1074-5521 JRNL PMID 9889151 JRNL DOI 10.1016/S1074-5521(99)80019-2 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.175 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.167 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1696 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 16956 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.168 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.163 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1566 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 15688 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1090 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 222 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1358.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 5447 REMARK 3 NUMBER OF RESTRAINTS : 4683 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.048 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.060 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.010 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.072 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1973) 201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, REMARK 3 J.APPL.CRYST. 28 (1995) 53-56 REMARK 4 REMARK 4 1B3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-DEC-98. REMARK 100 THE DEPOSITION ID IS D_1000000229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAY-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : SI CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17338 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : 0.05600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.19600 REMARK 200 R SYM FOR SHELL (I) : 0.25000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 11.81750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.01500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.15350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.01500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.81750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.15350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 17 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 47 CD - NE - CZ ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG B 47 NE - CZ - NH1 ANGL. DEV. = 3.9 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 TYR A 3 -137.21 -118.50 REMARK 500 MET A 67 41.70 -91.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 197 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 196 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 198 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 199 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AOP A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AOP B 1 REMARK 999 REMARK 999 SEQUENCE REMARK 999 MODRES: 1B3A AOP A 1() AMINOOXYPENTANE LINKED TO PRO2 VIA REMARK 999 OXIME BOND REMARK 999 MODRES: 1B3A AOP B 1() AMINOOXYPENTANE LINKED TO PRO2 VIA REMARK 999 OXIME BOND DBREF 1B3A A 2 68 UNP P13501 CCL5_HUMAN 10 76 DBREF 1B3A B 2 68 UNP P13501 CCL5_HUMAN 10 76 SEQRES 1 A 67 PRO TYR SER SER ASP THR THR PRO CYS CYS PHE ALA TYR SEQRES 2 A 67 ILE ALA ARG PRO LEU PRO ARG ALA HIS ILE LYS GLU TYR SEQRES 3 A 67 PHE TYR THR SER GLY LYS CYS SER ASN PRO ALA VAL VAL SEQRES 4 A 67 PHE VAL THR ARG LYS ASN ARG GLN VAL CYS ALA ASN PRO SEQRES 5 A 67 GLU LYS LYS TRP VAL ARG GLU TYR ILE ASN SER LEU GLU SEQRES 6 A 67 MET SER SEQRES 1 B 67 PRO TYR SER SER ASP THR THR PRO CYS CYS PHE ALA TYR SEQRES 2 B 67 ILE ALA ARG PRO LEU PRO ARG ALA HIS ILE LYS GLU TYR SEQRES 3 B 67 PHE TYR THR SER GLY LYS CYS SER ASN PRO ALA VAL VAL SEQRES 4 B 67 PHE VAL THR ARG LYS ASN ARG GLN VAL CYS ALA ASN PRO SEQRES 5 B 67 GLU LYS LYS TRP VAL ARG GLU TYR ILE ASN SER LEU GLU SEQRES 6 B 67 MET SER HET SO4 A 197 5 HET SO4 A 196 5 HET SO4 A 198 5 HET AOP A 1 10 HET SO4 B 199 5 HET AOP B 1 10 HETNAM SO4 SULFATE ION HETNAM AOP PENTYLOXYAMINO-ACETALDEHYDE FORMUL 3 SO4 4(O4 S 2-) FORMUL 6 AOP 2(C7 H15 N O2) FORMUL 9 HOH *222(H2 O) HELIX 1 1 ARG A 21 HIS A 23 5 3 HELIX 2 2 LYS A 56 GLU A 66 1 11 HELIX 3 3 ARG B 21 HIS B 23 5 3 HELIX 4 4 LYS B 56 GLU B 66 1 11 SHEET 1 A 3 GLN A 48 ALA A 51 0 SHEET 2 A 3 VAL A 39 THR A 43 -1 N PHE A 41 O VAL A 49 SHEET 3 A 3 ILE A 24 TYR A 29 -1 N PHE A 28 O VAL A 40 SHEET 1 B 3 GLN B 48 ALA B 51 0 SHEET 2 B 3 VAL B 39 THR B 43 -1 N PHE B 41 O VAL B 49 SHEET 3 B 3 ILE B 24 TYR B 29 -1 N PHE B 28 O VAL B 40 SSBOND 1 CYS A 10 CYS A 34 1555 1555 2.03 SSBOND 2 CYS A 11 CYS A 50 1555 1555 2.02 SSBOND 3 CYS B 10 CYS B 34 1555 1555 2.03 SSBOND 4 CYS B 11 CYS B 50 1555 1555 2.05 LINK C1 AOP A 1 N PRO A 2 1555 1555 1.33 LINK C1 AOP B 1 N PRO B 2 1555 1555 1.33 SITE 1 AC1 7 PRO A 9 PHE A 28 GLN A 48 HOH A1085 SITE 2 AC1 7 HOH A1091 ALA B 22 ILE B 24 SITE 1 AC2 8 HIS A 23 THR A 43 ARG A 44 LYS A 45 SITE 2 AC2 8 ARG A 47 SER A 68 HOH A1122 HOH B1130 SITE 1 AC3 9 SER A 31 GLY A 32 HOH A1100 HOH A1129 SITE 2 AC3 9 HOH A1160 HOH A1161 HOH A1169 SER B 31 SITE 3 AC3 9 GLY B 32 SITE 1 AC4 7 HIS B 23 THR B 43 ARG B 44 LYS B 45 SITE 2 AC4 7 ARG B 47 SER B 68 HOH B1066 SITE 1 AC5 8 PRO A 2 TYR A 3 HOH A1034 CYS B 11 SITE 2 AC5 8 PHE B 12 ALA B 13 TYR B 14 ASN B 36 SITE 1 AC6 7 PHE A 12 TYR A 14 HIS A 23 HOH A1124 SITE 2 AC6 7 HOH A1206 PRO B 2 HOH B1130 CRYST1 23.635 56.307 94.030 90.00 90.00 90.00 P 21 21 21 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 0.042310 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017760 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010635 0.00000 MTRIX1 1 -0.993225 0.114072 0.022194 29.97141 1 MTRIX2 1 0.079982 0.532445 0.842677 -13.80924 1 MTRIX3 1 0.084309 0.838743 -0.537961 20.89648 1