HEADER ICE-BINDING PROTEIN 25-OCT-96 1GZI TITLE CRYSTAL STRUCTURE OF TYPE III ANTIFREEZE PROTEIN FROM OCEAN POUT, AT TITLE 2 1.8 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HPLC-12 TYPE III ANTIFREEZE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 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 VARIANT: HPLC-12 COMPONENT; SOURCE 6 CELL_LINE: BL21; SOURCE 7 ORGAN: BLOOD; SOURCE 8 TISSUE: BLOOD SERUM; SOURCE 9 GENE: RECOMBINANT TYPE III AFP HPLC; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET22B; SOURCE 14 EXPRESSION_SYSTEM_GENE: RECOMBINANT TYPE III AFP HPLC FRACTION 12 KEYWDS ANTIFREEZE PROTEIN, OCEAN POUT, GLYCOPROTEIN, MACROZOARCES KEYWDS 2 AMERICANUS, ICE-BINDING PROTEIN, MULTIGENE FAMILY EXPDTA X-RAY DIFFRACTION AUTHOR A.A.ANTSON,S.LEWIS,D.I.ROPER,D.J.SMITH,R.E.HUBBARD REVDAT 4 07-FEB-24 1GZI 1 REMARK REVDAT 3 03-NOV-21 1GZI 1 SEQADV REVDAT 2 24-FEB-09 1GZI 1 VERSN REVDAT 1 17-SEP-97 1GZI 0 JRNL AUTH A.A.ANTSON,S.LEWIS,D.I.ROPER,D.J.SMITH,R.E.HUBBARD JRNL TITL THE STRUCTURE OF TYPE III ANTIFREEZE PROTEIN FROM OCEAN POUT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 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 2 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 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 5709 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 480 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 54 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.30 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.011 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.029 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.035 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.172 ; 0.200 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.190 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.255 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 5.100 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 17.600; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 7.200 ; 25.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.350 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.020 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.010 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.020 ; 6.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE FOLLOWING RESIDUES WERE MODELED IN TWO CONFORMATIONS: REMARK 3 VAL A 20 - SIDE CHAIN ATOMS. REMARK 3 SER A 42 - TWO CONFORMATIONS FOR THE SIDE CHAIN HYDROXYL. REMARK 4 REMARK 4 1GZI 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_1000173734. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 5.6 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 : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5155 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.20800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE, PH 5.6 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 16.27500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.76000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.76000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.27500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.65000 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 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 SER A 42 -6.49 79.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ALA A 64 12.85 REMARK 500 REMARK 500 REMARK: NULL DBREF 1GZI A 1 65 UNP P19614 ANPC_MACAM 1 66 SEQADV 1GZI A UNP P19614 PRO 64 DELETION SEQADV 1GZI ALA A 64 UNP P19614 PRO 65 ENGINEERED MUTATION SEQRES 1 A 65 ASN GLN ALA SER VAL VAL ALA ASN GLN LEU ILE PRO ILE SEQRES 2 A 65 ASN THR ALA LEU THR LEU VAL MET MET ARG SER GLU VAL SEQRES 3 A 65 VAL THR PRO VAL GLY ILE PRO ALA GLU ASP ILE PRO ARG SEQRES 4 A 65 LEU VAL SER MET GLN VAL ASN ARG ALA VAL PRO LEU GLY SEQRES 5 A 65 THR THR LEU MET PRO ASP MET VAL LYS GLY TYR ALA ALA FORMUL 2 HOH *54(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 ALA A 3 ALA A 7 0 SHEET 2 A 2 MET A 22 VAL A 26 -1 N GLU A 25 O SER A 4 CISPEP 1 THR A 28 PRO A 29 0 5.18 CRYST1 32.550 39.300 45.520 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 0.030722 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025445 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021968 0.00000