PDB Short entry for 1EQT HEADER CYTOKINE 06-APR-00 1EQT TITLE MET-RANTES COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL SPECIFIC RANTES PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SMALL INDUCIBLE CYTOKINE A5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BLOOD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PT7-7 KEYWDS CHEMOATTRACTANT, CYTOKINE, RANTES EXPDTA X-RAY DIFFRACTION AUTHOR D.M.HOOVER,J.SHAW,Z.GRYCZYNSKI,A.E.I.PROUDFOOT,T.WELLS REVDAT 3 09-AUG-23 1EQT 1 REMARK SEQADV REVDAT 2 24-FEB-09 1EQT 1 VERSN REVDAT 1 19-APR-00 1EQT 0 JRNL AUTH D.M.HOOVER,J.SHAW,Z.GRYCZYNSKI,A.E.I.PROUDFOOT,T.WELLS JRNL TITL THE CRYSTAL STRUCTURE OF MET-RANTES: COMPARISON WITH NATIVE JRNL TITL 2 RANTES AND AOP-RANTES JRNL REF PROTEIN PEPT.LETT. V. 7 73 2000 JRNL REFN ISSN 0929-8665 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.WILKEN,D.HOOVER,D.A.THOMPSON,P.N.BARLOW,H.MCSPARRON, REMARK 1 AUTH 2 L.PICARD,A.WLODAWER,J.LUBKOWSKI,S.B.KENT REMARK 1 TITL TOTAL CHEMICAL SYNTHESIS AND HIGH-RESOLUTION CRYSTAL REMARK 1 TITL 2 STRUCTURE OF THE POTENT ANTI-HIV PROTEIN AOP-RANTES REMARK 1 REF CHEM.BIOL. V. 6 43 1999 REMARK 1 REFN ISSN 1074-5521 REMARK 1 DOI 10.1016/S1074-5521(99)80019-2 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.E.PROUDFOOT,C.A.POWER,A.J.HOOGEWERF,M.O.MONTJOVENT, REMARK 1 AUTH 2 F.BORLAT,R.E.OFFORD,T.N.WELLS REMARK 1 TITL EXTENSION OF RECOMBINANT HUMAN RANTES BY THE RETENTION OF REMARK 1 TITL 2 THE INITIATING METHIONINE PRODUCES A POTENT ANTAGONIST REMARK 1 REF J.BIOL.CHEM. V. 271 2599 1996 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.271.5.2599 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 (%) : 84.2 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) : 0.178 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.186 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 165 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 17136 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.177 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 142 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 1428 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1084 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 187 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1281.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 513 REMARK 3 NUMBER OF RESTRAINTS : 451 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EQT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-00. REMARK 100 THE DEPOSITION ID IS D_1000010830. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-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) : 0.98 REMARK 200 MONOCHROMATOR : SI CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17136 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.3000 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 (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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: RANTES (NMR MODEL 1RTN) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 35000, AMMONIUM SULFATE, SODIUM REMARK 280 SUCCINATE, MES, SODIUM ACETATE, ETHANOL, PH 4.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295.0K 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 12.00950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.93150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.40450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.93150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.00950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.40450 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS LIKELY A DIMER CONSTRUCTED OF REMARK 300 BOTH CHAIN A AND B. 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 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 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 MET A 1 REMARK 465 MET B 1 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 - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 21 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES 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 198 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 199 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B3A RELATED DB: PDB REMARK 900 AOP-RANTES REMARK 999 REMARK 999 SEQUENCE REMARK 999 INITIATING MET RETAINED. DBREF 1EQT A 2 68 UNP P13501 CCL5_HUMAN 25 91 DBREF 1EQT B 2 68 UNP P13501 CCL5_HUMAN 25 91 SEQADV 1EQT MET A 1 UNP P13501 SEE REMARK 999 SEQADV 1EQT GLY A 2 UNP P13501 PRO 25 CONFLICT SEQADV 1EQT MET A 19 UNP P13501 LEU 42 CONFLICT SEQADV 1EQT MET B 1 UNP P13501 SEE REMARK 999 SEQADV 1EQT GLY B 2 UNP P13501 PRO 25 CONFLICT SEQADV 1EQT MET B 19 UNP P13501 LEU 42 CONFLICT SEQRES 1 A 68 MET GLY TYR SER SER ASP THR THR PRO CYS CYS PHE ALA SEQRES 2 A 68 TYR ILE ALA ARG PRO MET PRO ARG ALA HIS ILE LYS GLU SEQRES 3 A 68 TYR PHE TYR THR SER GLY LYS CYS SER ASN PRO ALA VAL SEQRES 4 A 68 VAL PHE VAL THR ARG LYS ASN ARG GLN VAL CYS ALA ASN SEQRES 5 A 68 PRO GLU LYS LYS TRP VAL ARG GLU TYR ILE ASN SER LEU SEQRES 6 A 68 GLU MET SER SEQRES 1 B 68 MET GLY TYR SER SER ASP THR THR PRO CYS CYS PHE ALA SEQRES 2 B 68 TYR ILE ALA ARG PRO MET PRO ARG ALA HIS ILE LYS GLU SEQRES 3 B 68 TYR PHE TYR THR SER GLY LYS CYS SER ASN PRO ALA VAL SEQRES 4 B 68 VAL PHE VAL THR ARG LYS ASN ARG GLN VAL CYS ALA ASN SEQRES 5 B 68 PRO GLU LYS LYS TRP VAL ARG GLU TYR ILE ASN SER LEU SEQRES 6 B 68 GLU MET SER HET SO4 A 198 5 HET SO4 B 199 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *187(H2 O) HELIX 1 1 PRO A 20 ALA A 22 5 3 HELIX 2 2 LYS A 55 MET A 67 1 13 HELIX 3 3 PRO B 20 ALA B 22 5 3 HELIX 4 4 LYS B 55 SER B 68 1 14 SHEET 1 A 2 THR A 8 CYS A 10 0 SHEET 2 A 2 THR B 8 CYS B 10 -1 O THR B 8 N CYS A 10 SHEET 1 B 3 ILE A 24 TYR A 29 0 SHEET 2 B 3 VAL A 39 THR A 43 -1 N VAL A 40 O PHE A 28 SHEET 3 B 3 GLN A 48 ALA A 51 -1 O VAL A 49 N PHE A 41 SHEET 1 C 3 ILE B 24 TYR B 29 0 SHEET 2 C 3 VAL B 39 THR B 43 -1 N VAL B 40 O PHE B 28 SHEET 3 C 3 GLN B 48 ALA B 51 -1 O VAL B 49 N PHE B 41 SSBOND 1 CYS A 10 CYS A 34 1555 1555 2.03 SSBOND 2 CYS A 11 CYS A 50 1555 1555 2.06 SSBOND 3 CYS B 10 CYS B 34 1555 1555 2.04 SSBOND 4 CYS B 11 CYS B 50 1555 1555 2.04 SITE 1 AC1 10 TYR A 3 SER A 31 GLY A 32 LYS A 33 SITE 2 AC1 10 HOH A1030 HOH A1116 HOH A1123 HOH A1125 SITE 3 AC1 10 SER B 31 GLY B 32 SITE 1 AC2 8 HIS B 23 THR B 43 ARG B 44 LYS B 45 SITE 2 AC2 8 ARG B 47 MET B 67 SER B 68 HOH B1095 CRYST1 24.019 56.809 93.863 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 0.041634 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017603 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010654 0.00000