PDB Short entry for 1B53 HEADER CHEMOKINE 11-JAN-99 1B53 TITLE NMR STRUCTURE OF HUMAN MIP-1A D26A, MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MIP-1A; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS CHEMOKINE, CYTOKINE, CHEMOTAXIS EXPDTA SOLUTION NMR AUTHOR J.P.WALTHO,L.D.HIGGINS,C.J.CRAVEN,P.TAN,T.DUDGEON REVDAT 5 03-NOV-21 1B53 1 SEQADV REVDAT 4 22-FEB-12 1B53 1 JRNL VERSN REVDAT 3 24-FEB-09 1B53 1 VERSN REVDAT 2 01-APR-03 1B53 1 JRNL REVDAT 1 22-JUL-99 1B53 0 JRNL AUTH L.G.CZAPLEWSKI,J.MCKEATING,C.J.CRAVEN,L.D.HIGGINS,V.APPAY, JRNL AUTH 2 A.BROWN,T.DUDGEON,L.A.HOWARD,T.MEYERS,J.OWEN,S.R.PALAN, JRNL AUTH 3 P.TAN,G.WILSON,N.R.WOODS,C.M.HEYWORTH,B.I.LORD,D.BROTHERTON, JRNL AUTH 4 R.CHRISTISON,S.CRAIG,S.CRIBBES,R.M.EDWARDS,S.J.EVANS, JRNL AUTH 5 R.GILBERT,P.MORGAN,E.RANDLE,N.SCHOFIELD,P.G.VARLEY,J.FISHER, JRNL AUTH 6 J.P.WALTHO,M.G.HUNTER JRNL TITL IDENTIFICATION OF AMINO ACID RESIDUES CRITICAL FOR JRNL TITL 2 AGGREGATION OF HUMAN CC CHEMOKINES MACROPHAGE INFLAMMATORY JRNL TITL 3 PROTEIN (MIP)-1ALPHA, MIP-1BETA, AND RANTES. JRNL TITL 4 CHARACTERIZATION OF ACTIVE DISAGGREGATED CHEMOKINE VARIANTS. JRNL REF J.BIOL.CHEM. V. 274 16077 1999 JRNL REFN ISSN 0021-9258 JRNL PMID 10347159 JRNL DOI 10.1074/JBC.274.23.16077 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 1B53 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171482. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : 3.5 REMARK 210 IONIC STRENGTH : NO ADDED SALT REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 10% H2O/90% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : ST; ARD HETERONUCLEAR TECHNIQUES REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING STARTING REMARK 210 FROM RANDOM ATOM POSITIONS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: MEAN STRUCTURE. THE STRUCTURE WAS DETERMINED USING TRIPLE REMARK 210 -RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELLED MIP-1A. REMARK 210 ADDITIONAL INTERMONOMER CONSTRAINTS WERE ACQUIRED USING A MIXED REMARK 210 13C/15N-12C/14N SAMPLE. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HB3 SER A 13 HB2 ALA B 4 1.12 REMARK 500 HB2 SER A 13 O ALA B 4 1.27 REMARK 500 HD2 PHE A 12 OG1 THR B 8 1.57 REMARK 500 CB SER A 13 O ALA B 4 2.17 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 TYR A 14 CB - CG - CD2 ANGL. DEV. = -10.6 DEGREES REMARK 500 TYR A 14 CD1 - CG - CD2 ANGL. DEV. = -67.5 DEGREES REMARK 500 TYR A 14 CB - CG - CD1 ANGL. DEV. = 15.0 DEGREES REMARK 500 TYR A 14 CG - CD1 - CE1 ANGL. DEV. = -44.0 DEGREES REMARK 500 TYR A 14 CG - CD2 - CE2 ANGL. DEV. = -45.7 DEGREES REMARK 500 TYR A 14 CD1 - CE1 - CZ ANGL. DEV. = -44.2 DEGREES REMARK 500 TYR A 14 CE1 - CZ - CE2 ANGL. DEV. = -68.8 DEGREES REMARK 500 TYR A 14 CZ - CE2 - CD2 ANGL. DEV. = -42.4 DEGREES REMARK 500 TYR B 14 CB - CG - CD2 ANGL. DEV. = -10.6 DEGREES REMARK 500 TYR B 14 CD1 - CG - CD2 ANGL. DEV. = -67.5 DEGREES REMARK 500 TYR B 14 CB - CG - CD1 ANGL. DEV. = 15.0 DEGREES REMARK 500 TYR B 14 CG - CD1 - CE1 ANGL. DEV. = -44.0 DEGREES REMARK 500 TYR B 14 CG - CD2 - CE2 ANGL. DEV. = -45.6 DEGREES REMARK 500 TYR B 14 CD1 - CE1 - CZ ANGL. DEV. = -44.2 DEGREES REMARK 500 TYR B 14 CE1 - CZ - CE2 ANGL. DEV. = -68.8 DEGREES REMARK 500 TYR B 14 CZ - CE2 - CD2 ANGL. DEV. = -42.4 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 LEU A 2 -155.36 -161.13 REMARK 500 ALA A 3 -142.75 -62.46 REMARK 500 THR A 6 126.00 160.24 REMARK 500 THR A 8 90.84 -53.22 REMARK 500 ALA A 9 108.43 -48.22 REMARK 500 CYS A 11 77.60 -101.23 REMARK 500 ALA A 25 -38.65 -149.50 REMARK 500 ALA A 26 -145.80 -109.34 REMARK 500 TYR A 27 -43.50 178.78 REMARK 500 PHE A 28 -173.53 46.99 REMARK 500 GLU A 29 39.01 -164.17 REMARK 500 THR A 30 -143.67 42.37 REMARK 500 SER A 31 -166.09 -177.77 REMARK 500 GLN A 33 -29.84 78.31 REMARK 500 LYS A 36 77.93 -116.01 REMARK 500 PRO A 37 31.03 -82.15 REMARK 500 THR A 43 159.53 -41.61 REMARK 500 SER A 46 25.53 45.87 REMARK 500 SER A 54 35.87 -166.73 REMARK 500 LEU A 67 64.08 171.42 REMARK 500 LEU B 2 -155.44 -161.18 REMARK 500 ALA B 3 -142.74 -62.40 REMARK 500 THR B 6 125.99 160.30 REMARK 500 THR B 8 90.85 -53.23 REMARK 500 ALA B 9 108.40 -48.14 REMARK 500 CYS B 11 77.62 -101.23 REMARK 500 ALA B 25 -38.64 -149.52 REMARK 500 ALA B 26 -145.77 -109.34 REMARK 500 TYR B 27 -43.46 178.76 REMARK 500 PHE B 28 -173.56 47.22 REMARK 500 GLU B 29 38.99 -164.21 REMARK 500 THR B 30 -143.68 42.39 REMARK 500 SER B 31 -166.09 -177.79 REMARK 500 GLN B 33 -29.84 78.28 REMARK 500 LYS B 36 77.89 -115.94 REMARK 500 PRO B 37 31.03 -82.11 REMARK 500 THR B 43 159.46 -41.59 REMARK 500 SER B 46 25.51 45.88 REMARK 500 SER B 54 35.91 -166.79 REMARK 500 LEU B 67 64.08 171.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 14 0.45 SIDE CHAIN REMARK 500 ARG A 45 0.28 SIDE CHAIN REMARK 500 ARG A 47 0.29 SIDE CHAIN REMARK 500 TYR B 14 0.45 SIDE CHAIN REMARK 500 ARG B 45 0.28 SIDE CHAIN REMARK 500 ARG B 47 0.29 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1B53 A 1 69 UNP P10147 CCL3_HUMAN 24 92 DBREF 1B53 B 1 69 UNP P10147 CCL3_HUMAN 24 92 SEQADV 1B53 ALA A 26 UNP P10147 ASP 49 ENGINEERED MUTATION SEQADV 1B53 ALA B 26 UNP P10147 ASP 49 ENGINEERED MUTATION SEQRES 1 A 69 SER LEU ALA ALA ASP THR PRO THR ALA CYS CYS PHE SER SEQRES 2 A 69 TYR THR SER ARG GLN ILE PRO GLN ASN PHE ILE ALA ALA SEQRES 3 A 69 TYR PHE GLU THR SER SER GLN CYS SER LYS PRO GLY VAL SEQRES 4 A 69 ILE PHE LEU THR LYS ARG SER ARG GLN VAL CYS ALA ASP SEQRES 5 A 69 PRO SER GLU GLU TRP VAL GLN LYS TYR VAL SER ASP LEU SEQRES 6 A 69 GLU LEU SER ALA SEQRES 1 B 69 SER LEU ALA ALA ASP THR PRO THR ALA CYS CYS PHE SER SEQRES 2 B 69 TYR THR SER ARG GLN ILE PRO GLN ASN PHE ILE ALA ALA SEQRES 3 B 69 TYR PHE GLU THR SER SER GLN CYS SER LYS PRO GLY VAL SEQRES 4 B 69 ILE PHE LEU THR LYS ARG SER ARG GLN VAL CYS ALA ASP SEQRES 5 B 69 PRO SER GLU GLU TRP VAL GLN LYS TYR VAL SER ASP LEU SEQRES 6 B 69 GLU LEU SER ALA HELIX 1 1 GLN A 21 PHE A 23 5 3 HELIX 2 2 VAL A 58 SER A 63 1 6 HELIX 3 3 GLN B 21 PHE B 23 5 3 HELIX 4 4 VAL B 58 SER B 63 1 6 SSBOND 1 CYS A 10 CYS A 34 1555 1555 2.02 SSBOND 2 CYS A 10 CYS B 10 1555 1555 2.72 SSBOND 3 CYS A 11 CYS A 50 1555 1555 2.02 SSBOND 4 CYS A 34 CYS B 10 1555 1555 2.95 SSBOND 5 CYS A 34 CYS B 34 1555 1555 2.97 SSBOND 6 CYS B 10 CYS B 34 1555 1555 2.02 SSBOND 7 CYS B 11 CYS B 50 1555 1555 2.02 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000