HEADER ANTIFREEZE PROTEIN 21-JAN-11 3QF6 TITLE NEUTRON STRUCTURE OF TYPE-III ANTIFREEZE PROTEIN ALLOWS THE TITLE 2 RECONSTRUCTION OF AFP-ICE INTERFACE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE-3 ICE-STRUCTURING PROTEIN HPLC 12; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ANTIFREEZE PROTEIN QAE(HPLC 12), ISP TYPE III HPLC 12; COMPND 5 ENGINEERED: 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_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS ICE BINDING PROTEIN, ANTIFREEZE PROTEIN EXPDTA NEUTRON DIFFRACTION AUTHOR E.I.HOWARD,M.P.BLAKELEY,M.HAERTLEIN,I.PETIT-HAERTLEIN,A.MITSCHLER, AUTHOR 2 S.J.FISHER,A.COUSIDO-SIAH,A.G.SALVAY,A.POPOV,C.MULLER-DIECKMANN, AUTHOR 3 T.PETROVA,A.PODJARNY REVDAT 5 20-MAR-24 3QF6 1 SEQADV REVDAT 4 28-MAR-18 3QF6 1 REMARK REVDAT 3 08-NOV-17 3QF6 1 REMARK REVDAT 2 29-JUN-11 3QF6 1 JRNL REVDAT 1 22-JUN-11 3QF6 0 JRNL AUTH E.I.HOWARD,M.P.BLAKELEY,M.HAERTLEIN,I.PETIT-HAERTLEIN, JRNL AUTH 2 A.MITSCHLER,S.J.FISHER,A.COUSIDO-SIAH,A.G.SALVAY,A.POPOV, JRNL AUTH 3 C.MULLER-DIECKMANN,T.PETROVA,A.PODJARNY JRNL TITL NEUTRON STRUCTURE OF TYPE-III ANTIFREEZE PROTEIN ALLOWS THE JRNL TITL 2 RECONSTRUCTION OF AFP-ICE INTERFACE. JRNL REF J.MOL.RECOGNIT. V. 24 724 2011 JRNL REFN ISSN 0952-3499 JRNL PMID 21472814 JRNL DOI 10.1002/JMR.1130 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 4792 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.680 REMARK 3 FREE R VALUE TEST SET COUNT : 480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.89 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 39.60 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.56980 REMARK 3 B22 (A**2) : 1.91180 REMARK 3 B33 (A**2) : 6.08850 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 1211 REMARK 3 ANGLE : 1.353 2063 REMARK 3 CHIRALITY : 0.078 96 REMARK 3 PLANARITY : 0.007 175 REMARK 3 DIHEDRAL : 14.468 299 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3QF6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063567. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 23-MAY-08 REMARK 230 TEMPERATURE (KELVIN) : 298.0 REMARK 230 PH : 4.80 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : LADI III REMARK 230 WAVELENGTH OR RANGE (A) : 3.18-4.22 REMARK 230 MONOCHROMATOR : NITI MULTILAYER FILTER REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : LADI III REMARK 230 INTENSITY-INTEGRATION SOFTWARE : LAUEGEN REMARK 230 DATA SCALING SOFTWARE : LSCALE, SCALA REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 4803 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 230 RESOLUTION RANGE LOW (A) : 29.950 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 230 DATA REDUNDANCY : 14.80 REMARK 230 R MERGE (I) : 0.14000 REMARK 230 R SYM (I) : NULL REMARK 230 <I/SIGMA(I)> FOR THE DATA SET : 17.5000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 230 COMPLETENESS FOR SHELL (%) : 71.4 REMARK 230 DATA REDUNDANCY IN SHELL : 5.80 REMARK 230 R MERGE FOR SHELL (I) : 0.19500 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 <I/SIGMA(I)> FOR SHELL : 5.500 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : PHENIX REMARK 230 STARTING MODEL: NULL REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M AMMONIUM SULFATE, 9% D8-GLYCEROL, REMARK 280 50MM SODIUM ACETATE, PD 5.2, PH 4.8, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 285K 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 16.36450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.26850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.56150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.26850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.36450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.56150 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ALA A 66 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 PRO A 64 CG CD REMARK 470 PRO A 65 CG CD REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 D1 DOD A 73 O DOD A 217 1.12 REMARK 500 O DOD A 84 D2 DOD A 268 1.17 REMARK 500 O DOD A 79 D2 DOD A 271 1.55 REMARK 500 O DOD A 94 D1 DOD A 231 1.56 REMARK 500 O DOD A 73 O DOD A 217 2.04 REMARK 500 O DOD A 84 O DOD A 268 2.04 REMARK 500 O DOD A 89 O DOD A 124 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 D1 DOD A 265 O DOD A 1003 3655 1.35 REMARK 500 REMARK 500 REMARK: NULL 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 PRO A 64 N - CA - CB ANGL. DEV. = 7.7 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 SER A 42 -4.75 81.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HG7 RELATED DB: PDB DBREF 3QF6 A 1 66 UNP P19614 ANP12_MACAM 1 66 SEQADV 3QF6 ASP A 35 UNP P19614 GLU 35 CONFLICT SEQRES 1 A 66 ASN GLN ALA SER VAL VAL ALA ASN GLN LEU ILE PRO ILE SEQRES 2 A 66 ASN THR ALA LEU THR LEU VAL MET MET ARG SER GLU VAL SEQRES 3 A 66 VAL THR PRO VAL GLY ILE PRO ALA ASP ASP ILE PRO ARG SEQRES 4 A 66 LEU VAL SER MET GLN VAL ASN ARG ALA VAL PRO LEU GLY SEQRES 5 A 66 THR THR LEU MET PRO ASP MET VAL LYS GLY TYR PRO PRO SEQRES 6 A 66 ALA FORMUL 2 DOD *73(D2 O) HELIX 1 1 THR A 18 VAL A 20 5 3 HELIX 2 2 PRO A 33 ASP A 35 5 3 HELIX 3 3 ASP A 36 VAL A 41 1 6 HELIX 4 4 MET A 56 VAL A 60 5 5 SHEET 1 A 2 SER A 4 ALA A 7 0 SHEET 2 A 2 MET A 22 GLU A 25 -1 O GLU A 25 N SER A 4 CISPEP 1 THR A 28 PRO A 29 0 -0.40 CISPEP 2 THR A 28 PRO A 29 0 -1.19 CRYST1 32.729 39.123 46.537 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 0.030554 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021488 0.00000