HEADER ANTIFREEZE PROTEIN 17-NOV-97 1OPS TITLE ICE-BINDING SURFACE ON A TYPE III ANTIFREEZE PROTEIN FROM OCEAN POUT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE III ANTIFREEZE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TYPE III AFP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MACROZOARCES AMERICANUS; SOURCE 3 ORGANISM_COMMON: OCEAN POUT; SOURCE 4 ORGANISM_TAXID: 8199; SOURCE 5 TISSUE: SERUM; SOURCE 6 OTHER_DETAILS: ISOFORM HPLC-3 KEYWDS ANTIFREEZE PROTEIN, ICE CRYSTAL GROWTH INHIBITION, PRETZEL FOLD, KEYWDS 2 GLYCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.S.C.YANG,W.-C.HON,S.BUBANKO,Y.XUE,J.SEETHARAMAN,C.L.HEW,F.SICHERI REVDAT 4 03-APR-24 1OPS 1 REMARK REVDAT 3 14-FEB-24 1OPS 1 SEQADV REVDAT 2 24-FEB-09 1OPS 1 VERSN REVDAT 1 20-MAY-98 1OPS 0 JRNL AUTH D.S.YANG,W.C.HON,S.BUBANKO,Y.XUE,J.SEETHARAMAN,C.L.HEW, JRNL AUTH 2 F.SICHERI JRNL TITL IDENTIFICATION OF THE ICE-BINDING SURFACE ON A TYPE III JRNL TITL 2 ANTIFREEZE PROTEIN WITH A "FLATNESS FUNCTION" ALGORITHM. JRNL REF BIOPHYS.J. V. 74 2142 1998 JRNL REFN ISSN 0006-3495 JRNL PMID 9591641 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER 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)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 82.6 REMARK 3 NUMBER OF REFLECTIONS : 3107 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) : 0.204 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 304 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.016 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 52.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 175 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 23 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 468 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 33 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.40 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.26 REMARK 3 LOW RESOLUTION CUTOFF (A) : 40.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.710 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.970 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.860 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.900 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.150 ; 2.500 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK ENT MODEL USED REMARK 4 REMARK 4 1OPS 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_1000175493. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAY-93 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 8.0 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : SUPPER DOUBLE FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3107 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.843 REMARK 200 STARTING MODEL: THE STARTING STRUCTURAL MODEL WAS DETERMINED FROM REMARK 200 A CRYSTAL GROWN WITH THE RECOMBINANT, SINGLY-IODINATED PROTEIN, REMARK 200 ISOFORM HPLC-6. THIS MODEL IS NOT YET AVAILABLE. REMARK 200 REMARK 200 REMARK: THE STRUCTURE WAS SOLVED BY THE METHOD OF ITERATIVE SINGLE REMARK 200 ANOMALOUS SCATTERING (B.C. WANG, (1985), METHODS ENZYMOL., 114, REMARK 200 P90-117). REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.0 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 20.39500 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: 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 DBREF 1OPS A 2 65 UNP P19608 ANP2_MACAM 1 64 SEQADV 1OPS ALA A 20 UNP P19608 VAL 19 CONFLICT SEQADV 1OPS LEU A 40 UNP P19608 ILE 39 CONFLICT SEQADV 1OPS LEU A 55 UNP P19608 ILE 54 CONFLICT SEQRES 1 A 64 SER GLN SER VAL VAL ALA THR GLN LEU ILE PRO MET ASN SEQRES 2 A 64 THR ALA LEU THR PRO ALA MET MET GLU GLY LYS VAL THR SEQRES 3 A 64 ASN PRO ILE GLY ILE PRO PHE ALA GLU MET SER GLN LEU SEQRES 4 A 64 VAL GLY LYS GLN VAL ASN THR PRO VAL ALA LYS GLY GLN SEQRES 5 A 64 THR LEU MET PRO ASN MET VAL LYS THR TYR ALA ALA FORMUL 2 HOH *33(H2 O) HELIX 1 1 PRO A 19 MET A 21 5 3 HELIX 2 2 PHE A 34 GLN A 39 5 6 HELIX 3 3 PRO A 57 MET A 59 5 3 SHEET 1 A 2 SER A 4 ALA A 7 0 SHEET 2 A 2 MET A 22 LYS A 25 -1 N LYS A 25 O SER A 4 CISPEP 1 ASN A 28 PRO A 29 0 -0.48 CRYST1 23.060 40.790 29.990 90.00 100.60 90.00 P 1 21 1 2 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 0.043365 0.000000 0.008116 0.00000 SCALE2 0.000000 0.024516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033923 0.00000