HEADER ANTIFREEZE PROTEIN 21-JAN-99 1EKL TITLE TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 E35K COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (ANTIFREEZE PROTEIN TYPE III); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TYPE III ANTIFREEZE PROTEIN QAE ISOFORM; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MACROZOARCES AMERICANUS; SOURCE 3 ORGANISM_COMMON: OCEAN POUT; SOURCE 4 ORGANISM_TAXID: 8199; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PT7-7F KEYWDS ANTIFREEZE PROTEIN, MUTANT, ICE BINDING PROTEIN, THERMAL HYSTERESIS KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.P.GRAETHER,C.I.DELUCA,J.BAARDSNES,G.A.HILL,P.L.DAVIES,Z.JIA REVDAT 5 09-AUG-23 1EKL 1 REMARK REVDAT 4 03-NOV-21 1EKL 1 SEQADV REVDAT 3 24-FEB-09 1EKL 1 VERSN REVDAT 2 31-AUG-04 1EKL 1 COMPND JRNL REMARK FORMUL REVDAT 2 2 1 SCALE2 HETATM MASTER SOURCE REVDAT 1 29-APR-99 1EKL 0 JRNL AUTH S.P.GRAETHER,C.I.DELUCA,J.BAARDSNES,G.A.HILL,P.L.DAVIES, JRNL AUTH 2 Z.JIA JRNL TITL QUANTITATIVE AND QUALITATIVE ANALYSIS OF TYPE III ANTIFREEZE JRNL TITL 2 PROTEIN STRUCTURE AND FUNCTION. JRNL REF J.BIOL.CHEM. V. 274 11842 1999 JRNL REFN ISSN 0021-9258 JRNL PMID 10207002 JRNL DOI 10.1074/JBC.274.17.11842 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.I.DELUCA,P.L.DAVIES,Q.YE,Z.JIA REMARK 1 TITL THE EFFECTS OF STERIC MUTATIONS ON THE STRUCTURE OF TYPE III REMARK 1 TITL 2 ANTIFREEZE PROTEIN AND ITS INTERACTION WITH ICE REMARK 1 REF J.MOL.BIOL. V. 275 515 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 9466928 REMARK 1 DOI 10.1006/JMBI.1997.1482 REMARK 1 REFERENCE 2 REMARK 1 AUTH Z.JIA,C.I.DELUCA,H.CHAO,P.L.DAVIES REMARK 1 TITL STRUCTURAL BASIS FOR THE BINDING OF A GLOBULAR ANTIFREEZE REMARK 1 TITL 2 PROTEIN TO ICE REMARK 1 REF NATURE V. 384 285 1996 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 3 REMARK 1 AUTH Z.JIA,C.I.DELUCA,P.L.DAVIES REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC REMARK 1 TITL 2 STUDIES ON TYPE III ANTIFREEZE PROTEIN REMARK 1 REF PROTEIN SCI. V. 4 1236 1995 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 4 REMARK 1 AUTH H.CHAO,P.L.DAVIES,B.D.SYKES,F.D.SONNICHSEN REMARK 1 TITL USE OF PROLINE MUTANTS TO HELP SOLVE THE NMR SOLUTION REMARK 1 TITL 2 STRUCTURE OF TYPE III ANTIFREEZE PROTEIN REMARK 1 REF PROTEIN SCI. V. 2 1411 1993 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 5 REMARK 1 AUTH C.L.HEW,N.C.WANG,S.JOSHI,G.L.FLETCHER,G.K.SCOTT,P.H.HAYES, REMARK 1 AUTH 2 B.BUETTNER,P.L.DAVIES REMARK 1 TITL MULTIPLE GENES PROVIDE THE BASIS FOR ANTIFREEZE PROTEIN REMARK 1 TITL 2 DIVERSITY AND DOSAGE IN THE OCEAN POUT, MACROZOARCES REMARK 1 TITL 3 AMERICANUS REMARK 1 REF J.BIOL.CHEM. V. 263 12049 1988 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.0 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 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) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 7479 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 402 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.72 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 861 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 49 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 482 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.40 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) : 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) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 2.861 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.176 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 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-99. REMARK 100 THE DEPOSITION ID IS D_1000000355. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5.5 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 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7562 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 1MSI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.5 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 16.27200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.30750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.44650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.30750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.27200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.44650 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 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 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 1 CG OD1 ND2 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 39 NE - CZ - NH2 ANGL. DEV. = -3.6 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 ASN A 1 4.01 53.82 REMARK 500 REMARK 500 REMARK: NULL DBREF 1EKL A 1 65 UNP P19614 ANPC_MACAM 1 65 SEQADV 1EKL LYS A 35 UNP P19614 GLU 35 ENGINEERED MUTATION SEQADV 1EKL ALA A 64 UNP P19614 PRO 64 ENGINEERED MUTATION SEQADV 1EKL ALA A 65 UNP P19614 PRO 65 ENGINEERED MUTATION SEQRES 1 A 66 ALA ASN GLN ALA SER VAL VAL ALA ASN GLN LEU ILE PRO SEQRES 2 A 66 ILE ASN THR ALA LEU THR LEU VAL MET MET ARG SER GLU SEQRES 3 A 66 VAL VAL THR PRO VAL GLY ILE PRO ALA LYS ASP ILE PRO SEQRES 4 A 66 ARG LEU VAL SER MET GLN VAL ASN ARG ALA VAL PRO LEU SEQRES 5 A 66 GLY THR THR LEU MET PRO ASP MET VAL LYS GLY TYR ALA SEQRES 6 A 66 ALA FORMUL 2 HOH *61(H2 O) HELIX 1 1 LEU A 19 MET A 21 5 3 HELIX 2 2 ALA A 34 LEU A 40 5 7 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 GLU A 25 -1 N GLU A 25 O SER A 4 CISPEP 1 THR A 28 PRO A 29 0 -4.14 CRYST1 32.544 38.893 46.615 90.00 90.00 90.00 P 21 21 21 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 0.030728 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025712 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021452 0.00000