PDB Short entry for 1UCS HEADER ANTIFREEZE PROTEIN 21-APR-03 1UCS TITLE TYPE III ANTIFREEZE PROTEIN RD1 FROM AN ANTARCTIC EEL POUT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIFREEZE PEPTIDE RD1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TYPE III ANTIFREEZE PROTEIN RD1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LYCODICHTHYS DEARBORNI; SOURCE 3 ORGANISM_COMMON: ANTARCTIC EEL POUT; SOURCE 4 ORGANISM_TAXID: 8201 KEYWDS SMALL BETA BARREL, PRETZEL FOLD, ANTIFREEZE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.-P.KO,H.ROBINSON,Y.-G.GAO,C.-H.C.CHENG,A.L.DEVRIES,A.H.-J.WANG REVDAT 3 06-NOV-19 1UCS 1 JRNL REVDAT 2 24-FEB-09 1UCS 1 VERSN REVDAT 1 06-MAY-03 1UCS 0 JRNL AUTH T.P.KO,H.ROBINSON,Y.G.GAO,C.H.CHENG,A.L.DEVRIES,A.H.WANG JRNL TITL THE REFINED CRYSTAL STRUCTURE OF AN EEL POUT TYPE III JRNL TITL 2 ANTIFREEZE PROTEIN RD1 AT 0.62-A RESOLUTION REVEALS JRNL TITL 3 STRUCTURAL MICROHETEROGENEITY OF PROTEIN AND SOLVATION. JRNL REF BIOPHYS.J. V. 84 1228 2003 JRNL REFN ISSN 0006-3495 JRNL PMID 12547803 JRNL DOI 10.1016/S0006-3495(03)74938-8 REMARK 2 REMARK 2 RESOLUTION. 0.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.139 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.137 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 5902 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 127291 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 479 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 240 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ANISOTROPIC MODEL WAS USED IN REFINEMENT AND REMARK 3 THEN THE CONVERTED TO ISOTROPIC B VALUES REMARK 4 REMARK 4 1UCS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000005684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-00 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.6668 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 118502 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.620 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 (%) : 94.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.65300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: A POLYPEPTIDE MODEL DERIVED FROM NMR EXPERIMENTS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 11.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS-HCL, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K 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 16.25050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.32000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.75100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.32000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.25050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.75100 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: 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 ASN A 1 CB - CA - C ANGL. DEV. = 13.0 DEGREES REMARK 500 GLU A 35 OE1 - CD - OE2 ANGL. DEV. = -7.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MSI RELATED DB: PDB REMARK 900 HOMOLOGOUS PROTEIN SIMILAR CRYSTAL FORM REMARK 900 RELATED ID: 1HG7 RELATED DB: PDB REMARK 900 HOMOLOGOUS PROTEIN SIMILAR CRYSTAL FORM REMARK 900 RELATED ID: 1OPS RELATED DB: PDB REMARK 900 HOMOLOGOUS PROTEIN DIFFERENT CRYSTAL FORM DBREF 1UCS A 1 64 UNP P35751 ANP1_RHIDE 1 64 SEQRES 1 A 64 ASN LYS ALA SER VAL VAL ALA ASN GLN LEU ILE PRO ILE SEQRES 2 A 64 ASN THR ALA LEU THR LEU ILE MET MET LYS ALA GLU VAL SEQRES 3 A 64 VAL THR PRO MET GLY ILE PRO ALA GLU GLU ILE PRO LYS SEQRES 4 A 64 LEU VAL GLY MET GLN VAL ASN ARG ALA VAL PRO LEU GLY SEQRES 5 A 64 THR THR LEU MET PRO ASP MET VAL LYS ASN TYR GLU FORMUL 2 HOH *240(H2 O) HELIX 1 1 THR A 18 ILE A 20 5 3 HELIX 2 2 PRO A 33 GLU A 35 5 3 HELIX 3 3 GLU 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 -3.23 CRYST1 32.501 39.502 44.640 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 0.030768 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022401 0.00000