HEADER METAL TRANSPORT 08-JUN-00 1F4Q TITLE CRYSTAL STRUCTURE OF APO GRANCALCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GRANCALCIN; COMPND 3 CHAIN: A, B; 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: PGEX2T KEYWDS PENTA-EF-HAND PROTEIN, CALCIUM BINDING PROTEIN, METAL TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.JIA,Q.HAN,N.BORREGAARD,K.LOLLIKE,M.CYGLER REVDAT 3 07-FEB-24 1F4Q 1 SEQADV REVDAT 2 24-FEB-09 1F4Q 1 VERSN REVDAT 1 27-SEP-00 1F4Q 0 JRNL AUTH J.JIA,Q.HAN,N.BORREGAARD,K.LOLLIKE,M.CYGLER JRNL TITL CRYSTAL STRUCTURE OF HUMAN GRANCALCIN, A MEMBER OF THE JRNL TITL 2 PENTA-EF-HAND PROTEIN FAMILY. JRNL REF J.MOL.BIOL. V. 300 1271 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10903868 JRNL DOI 10.1006/JMBI.2000.3925 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Q.HAN,J.JIA,Y.LI,K.LOLLIKE,M.CYGLER REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF HUMAN REMARK 1 TITL 2 GRANCALCIN, A NOVEL CYTOSOLIC CA2+-BINDING PROTEIN PRESENT REMARK 1 TITL 3 IN LEUKOCYTES REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 56 772 2000 REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 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) (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 25452 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1997 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 : 2603 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.60 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.020 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 1F4Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011240. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-99 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00899 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25454 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 20.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21400 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 (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, SODIUM CHLORIDE, REMARK 280 AMMONIUM PHOSPHATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 40.55000 REMARK 290 SMTRY3 2 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: 3920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 133 REMARK 465 ASP A 134 REMARK 465 GLY A 135 REMARK 465 SER A 136 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 HIS A 105 70.28 48.81 REMARK 500 SER B 136 -67.14 27.04 REMARK 500 ARG B 154 77.92 -119.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F4O RELATED DB: PDB REMARK 900 GRANCALCIN WITH CALCIUM BOUND DBREF 1F4Q A 53 217 UNP P28676 GRAN_HUMAN 53 217 DBREF 1F4Q B 53 217 UNP P28676 GRAN_HUMAN 53 217 SEQADV 1F4Q LYS A 193 UNP P28676 ARG 193 CONFLICT SEQADV 1F4Q ASP A 204 UNP P28676 ASN 204 CONFLICT SEQADV 1F4Q LYS B 193 UNP P28676 ARG 193 CONFLICT SEQADV 1F4Q ASP B 204 UNP P28676 ASN 204 CONFLICT SEQRES 1 A 165 SER VAL TYR THR TYR PHE SER ALA VAL ALA GLY GLN ASP SEQRES 2 A 165 GLY GLU VAL ASP ALA GLU GLU LEU GLN ARG CYS LEU THR SEQRES 3 A 165 GLN SER GLY ILE ASN GLY THR TYR SER PRO PHE SER LEU SEQRES 4 A 165 GLU THR CYS ARG ILE MET ILE ALA MET LEU ASP ARG ASP SEQRES 5 A 165 HIS THR GLY LYS MET GLY PHE ASN ALA PHE LYS GLU LEU SEQRES 6 A 165 TRP ALA ALA LEU ASN ALA TRP LYS GLU ASN PHE MET THR SEQRES 7 A 165 VAL ASP GLN ASP GLY SER GLY THR VAL GLU HIS HIS GLU SEQRES 8 A 165 LEU ARG GLN ALA ILE GLY LEU MET GLY TYR ARG LEU SER SEQRES 9 A 165 PRO GLN THR LEU THR THR ILE VAL LYS ARG TYR SER LYS SEQRES 10 A 165 ASN GLY ARG ILE PHE PHE ASP ASP TYR VAL ALA CYS CYS SEQRES 11 A 165 VAL LYS LEU ARG ALA LEU THR ASP PHE PHE LYS LYS ARG SEQRES 12 A 165 ASP HIS LEU GLN GLN GLY SER ALA ASP PHE ILE TYR ASP SEQRES 13 A 165 ASP PHE LEU GLN GLY THR MET ALA ILE SEQRES 1 B 165 SER VAL TYR THR TYR PHE SER ALA VAL ALA GLY GLN ASP SEQRES 2 B 165 GLY GLU VAL ASP ALA GLU GLU LEU GLN ARG CYS LEU THR SEQRES 3 B 165 GLN SER GLY ILE ASN GLY THR TYR SER PRO PHE SER LEU SEQRES 4 B 165 GLU THR CYS ARG ILE MET ILE ALA MET LEU ASP ARG ASP SEQRES 5 B 165 HIS THR GLY LYS MET GLY PHE ASN ALA PHE LYS GLU LEU SEQRES 6 B 165 TRP ALA ALA LEU ASN ALA TRP LYS GLU ASN PHE MET THR SEQRES 7 B 165 VAL ASP GLN ASP GLY SER GLY THR VAL GLU HIS HIS GLU SEQRES 8 B 165 LEU ARG GLN ALA ILE GLY LEU MET GLY TYR ARG LEU SER SEQRES 9 B 165 PRO GLN THR LEU THR THR ILE VAL LYS ARG TYR SER LYS SEQRES 10 B 165 ASN GLY ARG ILE PHE PHE ASP ASP TYR VAL ALA CYS CYS SEQRES 11 B 165 VAL LYS LEU ARG ALA LEU THR ASP PHE PHE LYS LYS ARG SEQRES 12 B 165 ASP HIS LEU GLN GLN GLY SER ALA ASP PHE ILE TYR ASP SEQRES 13 B 165 ASP PHE LEU GLN GLY THR MET ALA ILE FORMUL 3 HOH *175(H2 O) HELIX 1 1 SER A 53 ALA A 62 1 10 HELIX 2 2 ASP A 69 GLY A 81 1 13 HELIX 3 3 SER A 90 ASP A 102 1 13 HELIX 4 4 GLY A 110 VAL A 131 1 22 HELIX 5 5 HIS A 141 MET A 151 1 11 HELIX 6 6 SER A 156 SER A 168 1 13 HELIX 7 7 PHE A 175 ASP A 196 1 22 HELIX 8 8 TYR A 207 ILE A 217 1 11 HELIX 9 9 SER B 53 ALA B 62 1 10 HELIX 10 10 ASP B 69 GLY B 81 1 13 HELIX 11 11 SER B 90 ASP B 102 1 13 HELIX 12 12 GLY B 110 ASP B 132 1 23 HELIX 13 13 HIS B 141 MET B 151 1 11 HELIX 14 14 SER B 156 SER B 168 1 13 HELIX 15 15 PHE B 175 ASP B 196 1 22 HELIX 16 16 TYR B 207 ILE B 217 1 11 SHEET 1 A 2 THR A 138 GLU A 140 0 SHEET 2 A 2 ARG A 172 PHE A 174 -1 N ILE A 173 O VAL A 139 SHEET 1 B 2 SER A 202 ILE A 206 0 SHEET 2 B 2 SER B 202 ILE B 206 -1 O ALA B 203 N PHE A 205 SHEET 1 C 2 THR B 138 GLU B 140 0 SHEET 2 C 2 ARG B 172 PHE B 174 -1 N ILE B 173 O VAL B 139 CRYST1 48.400 81.100 46.700 90.00 111.30 90.00 P 1 21 1 4 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 0.020653 0.000000 0.008052 0.00000 SCALE2 0.000000 0.012324 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022968 0.00000