HEADER METAL BINDING PROTEIN 25-JAN-02 1J55 TITLE THE CRYSTAL STRUCTURE OF CA+-BOUND HUMAN S100P DETERMINED AT 2.0A TITLE 2 RESOLUTION BY X-RAY COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-100P PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,G.WANG,Y.DING,Z.WANG,R.BARRACLOUGH,P.S.RUDLAND,D.G.FERNIG, AUTHOR 2 Z.RAO REVDAT 4 27-DEC-23 1J55 1 REMARK LINK REVDAT 3 13-JUL-11 1J55 1 VERSN REVDAT 2 24-FEB-09 1J55 1 VERSN REVDAT 1 07-JAN-03 1J55 0 JRNL AUTH H.ZHANG,G.WANG,Y.DING,Z.WANG,R.BARRACLOUGH,P.S.RUDLAND, JRNL AUTH 2 D.G.FERNIG,Z.RAO JRNL TITL THE CRYSTAL STRUCTURE AT 2A RESOLUTION OF THE CA2+-BINDING JRNL TITL 2 PROTEIN S100P JRNL REF J.MOL.BIOL. V. 325 785 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12507480 JRNL DOI 10.1016/S0022-2836(02)01278-0 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 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) (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 6226 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) : 0.214 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 680 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 : 673 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 46 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 1.680 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: CNS REMARK 4 REMARK 4 1J55 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000001625. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57916 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.40300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 41.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, SODIUM CITRATE, CALCIUM REMARK 280 CHLORIDE, PH 6.5, EVAPORATION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 23.80500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.41350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.41350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.90250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.41350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.41350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.70750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.41350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.41350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 11.90250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.41350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.41350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.70750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 23.80500 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 KCAL/MOL 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 BIOMT1 2 0.000000 -1.000000 0.000000 60.82700 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 60.82700 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 23.80500 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 GLN A 46 REMARK 465 SER A 47 REMARK 465 GLY A 48 REMARK 465 LYS A 49 REMARK 465 ASP A 50 REMARK 465 LYS A 51 REMARK 465 LYS A 95 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 19 O REMARK 620 2 GLU A 22 O 121.2 REMARK 620 3 SER A 24 O 80.8 98.2 REMARK 620 4 THR A 27 O 82.3 156.2 89.2 REMARK 620 5 GLU A 32 OE2 73.2 76.7 145.0 109.5 REMARK 620 6 GLU A 32 OE1 103.0 94.5 162.4 74.4 50.4 REMARK 620 7 HOH A 133 O 155.5 80.7 85.4 77.4 126.7 84.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 102 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 62 OD1 REMARK 620 2 ASN A 64 OD1 74.7 REMARK 620 3 ASP A 66 OD1 82.8 80.8 REMARK 620 4 GLN A 68 O 93.3 158.3 79.7 REMARK 620 5 GLU A 73 OE1 114.3 126.5 149.9 74.9 REMARK 620 6 GLU A 73 OE2 88.3 78.8 159.3 119.6 50.5 REMARK 620 7 HOH A 103 O 162.9 90.6 86.4 97.7 81.3 97.4 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 102 DBREF 1J55 A 1 95 UNP P25815 S100P_HUMAN 1 95 SEQRES 1 A 95 MET THR GLU LEU GLU THR ALA MET GLY MET ILE ILE ASP SEQRES 2 A 95 VAL PHE SER ARG TYR SER GLY SER GLU GLY SER THR GLN SEQRES 3 A 95 THR LEU THR LYS GLY GLU LEU LYS VAL LEU MET GLU LYS SEQRES 4 A 95 GLU LEU PRO GLY PHE LEU GLN SER GLY LYS ASP LYS ASP SEQRES 5 A 95 ALA VAL ASP LYS LEU LEU LYS ASP LEU ASP ALA ASN GLY SEQRES 6 A 95 ASP ALA GLN VAL ASP PHE SER GLU PHE ILE VAL PHE VAL SEQRES 7 A 95 ALA ALA ILE THR SER ALA CYS HIS LYS TYR PHE GLU LYS SEQRES 8 A 95 ALA GLY LEU LYS HET CA A 101 1 HET CA A 102 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) FORMUL 4 HOH *46(H2 O) HELIX 1 1 THR A 2 SER A 19 1 18 HELIX 2 2 THR A 29 LEU A 41 1 13 HELIX 3 3 ASP A 52 ASP A 62 1 11 HELIX 4 4 PHE A 71 GLY A 93 1 23 SHEET 1 A 2 THR A 27 LEU A 28 0 SHEET 2 A 2 VAL A 69 ASP A 70 -1 O VAL A 69 N LEU A 28 LINK O SER A 19 CA CA A 101 1555 1555 2.44 LINK O GLU A 22 CA CA A 101 1555 1555 2.31 LINK O SER A 24 CA CA A 101 1555 1555 2.30 LINK O THR A 27 CA CA A 101 1555 1555 2.41 LINK OE2 GLU A 32 CA CA A 101 1555 1555 2.70 LINK OE1 GLU A 32 CA CA A 101 1555 1555 2.39 LINK OD1 ASP A 62 CA CA A 102 1555 1555 2.29 LINK OD1 ASN A 64 CA CA A 102 1555 1555 2.29 LINK OD1 ASP A 66 CA CA A 102 1555 1555 2.34 LINK O GLN A 68 CA CA A 102 1555 1555 2.33 LINK OE1 GLU A 73 CA CA A 102 1555 1555 2.64 LINK OE2 GLU A 73 CA CA A 102 1555 1555 2.50 LINK CA CA A 101 O HOH A 133 1555 1555 2.32 LINK CA CA A 102 O HOH A 103 1555 1555 2.48 SITE 1 AC1 6 SER A 19 GLU A 22 SER A 24 THR A 27 SITE 2 AC1 6 GLU A 32 HOH A 133 SITE 1 AC2 6 ASP A 62 ASN A 64 ASP A 66 GLN A 68 SITE 2 AC2 6 GLU A 73 HOH A 103 CRYST1 60.827 60.827 47.610 90.00 90.00 90.00 P 41 21 2 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 0.016440 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016440 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021004 0.00000