HEADER ANTIFREEZE PROTEIN 10-MAY-00 1EZG TITLE CRYSTAL STRUCTURE OF ANTIFREEZE PROTEIN FROM THE BEETLE, TENEBRIO TITLE 2 MOLITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMAL HYSTERESIS PROTEIN ISOFORM YL-1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TENEBRIO MOLITOR; SOURCE 3 ORGANISM_COMMON: YELLOW MEALWORM; SOURCE 4 ORGANISM_TAXID: 7067; SOURCE 5 GENE: CDNA FROM FAT BODY LIBRARY; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET20B; SOURCE 11 OTHER_DETAILS: LARVAE HEMOLYMPH KEYWDS INSECT ANTIFREEZE PROTEIN, THERMAL HYSTERESIS, TENEBRIO MOLITOR, KEYWDS 2 IODINATION, RIGHT-HANDED BETA-HELIX, TMAFP, ANTIFREEZE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.-C.LIOU,A.TOCILJ,P.L.DAVIES,Z.JIA REVDAT 4 30-OCT-24 1EZG 1 REMARK REVDAT 3 24-FEB-09 1EZG 1 VERSN REVDAT 2 01-APR-03 1EZG 1 JRNL REVDAT 1 09-AUG-00 1EZG 0 JRNL AUTH Y.C.LIOU,A.TOCILJ,P.L.DAVIES,Z.JIA JRNL TITL MIMICRY OF ICE STRUCTURE BY SURFACE HYDROXYLS AND WATER OF A JRNL TITL 2 BETA-HELIX ANTIFREEZE PROTEIN. JRNL REF NATURE V. 406 322 2000 JRNL REFN ISSN 0028-0836 JRNL PMID 10917536 JRNL DOI 10.1038/35018604 REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : 0.160 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.160 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3072 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 133370 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 : 1106 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 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) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 2.154 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: NULL REMARK 4 REMARK 4 1EZG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-00. REMARK 100 THE DEPOSITION ID IS D_1000011057. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91 REMARK 200 MONOCHROMATOR : NULL 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32557 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.20800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM CITRA, COBALT REMARK 280 CHLORIDEE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.42000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.71000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.56500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 8.85500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 44.27500 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 300 REMARK: IN SOLUTION, IT IS MONOMER. BUT IT IS A DIMER IN CRYSTAL. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 84 REMARK 465 HIS A 85 REMARK 465 GLY B 84 REMARK 465 HIS B 85 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 ASP B 45 CB - CG - OD1 ANGL. DEV. = 6.8 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 B 21 101.87 -163.77 REMARK 500 CYS B 34 57.72 -90.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EWW RELATED DB: PDB DBREF 1EZG A 2 85 UNP O16119 O16119_TENMO 29 112 DBREF 1EZG B 2 85 UNP O16119 O16119_TENMO 29 112 SEQRES 1 A 84 GLN CYS THR GLY GLY ALA ASP CYS THR SER CYS THR GLY SEQRES 2 A 84 ALA CYS THR GLY CYS GLY ASN CYS PRO ASN ALA VAL THR SEQRES 3 A 84 CYS THR ASN SER GLN HIS CYS VAL LYS ALA ASN THR CYS SEQRES 4 A 84 THR GLY SER THR ASP CYS ASN THR ALA GLN THR CYS THR SEQRES 5 A 84 ASN SER LYS ASP CYS PHE GLU ALA ASN THR CYS THR ASP SEQRES 6 A 84 SER THR ASN CYS TYR LYS ALA THR ALA CYS THR ASN SER SEQRES 7 A 84 SER GLY CYS PRO GLY HIS SEQRES 1 B 84 GLN CYS THR GLY GLY ALA ASP CYS THR SER CYS THR GLY SEQRES 2 B 84 ALA CYS THR GLY CYS GLY ASN CYS PRO ASN ALA VAL THR SEQRES 3 B 84 CYS THR ASN SER GLN HIS CYS VAL LYS ALA ASN THR CYS SEQRES 4 B 84 THR GLY SER THR ASP CYS ASN THR ALA GLN THR CYS THR SEQRES 5 B 84 ASN SER LYS ASP CYS PHE GLU ALA ASN THR CYS THR ASP SEQRES 6 B 84 SER THR ASN CYS TYR LYS ALA THR ALA CYS THR ASN SER SEQRES 7 B 84 SER GLY CYS PRO GLY HIS SHEET 1 A 6 ALA A 15 THR A 17 0 SHEET 2 A 6 THR A 27 THR A 29 1 O THR A 27 N CYS A 16 SHEET 3 A 6 THR A 39 THR A 41 1 O THR A 39 N CYS A 28 SHEET 4 A 6 THR A 51 THR A 53 1 O THR A 51 N CYS A 40 SHEET 5 A 6 THR A 63 THR A 65 1 O THR A 63 N CYS A 52 SHEET 6 A 6 ALA A 75 THR A 77 1 O ALA A 75 N CYS A 64 SHEET 1 B 6 ALA B 15 THR B 17 0 SHEET 2 B 6 THR B 27 THR B 29 1 O THR B 27 N CYS B 16 SHEET 3 B 6 THR B 39 THR B 41 1 O THR B 39 N CYS B 28 SHEET 4 B 6 THR B 51 THR B 53 1 O THR B 51 N CYS B 40 SHEET 5 B 6 THR B 63 THR B 65 1 O THR B 63 N CYS B 52 SHEET 6 B 6 ALA B 75 THR B 77 1 O ALA B 75 N CYS B 64 SSBOND 1 CYS A 3 CYS A 12 1555 1555 2.02 SSBOND 2 CYS A 9 CYS A 19 1555 1555 2.04 SSBOND 3 CYS A 16 CYS A 22 1555 1555 2.06 SSBOND 4 CYS A 28 CYS A 34 1555 1555 2.06 SSBOND 5 CYS A 40 CYS A 46 1555 1555 2.04 SSBOND 6 CYS A 52 CYS A 58 1555 1555 2.05 SSBOND 7 CYS A 64 CYS A 70 1555 1555 2.01 SSBOND 8 CYS A 76 CYS A 82 1555 1555 2.03 SSBOND 9 CYS B 3 CYS B 12 1555 1555 2.08 SSBOND 10 CYS B 9 CYS B 19 1555 1555 2.02 SSBOND 11 CYS B 16 CYS B 22 1555 1555 2.05 SSBOND 12 CYS B 28 CYS B 34 1555 1555 2.05 SSBOND 13 CYS B 40 CYS B 46 1555 1555 2.05 SSBOND 14 CYS B 52 CYS B 58 1555 1555 2.04 SSBOND 15 CYS B 64 CYS B 70 1555 1555 2.05 SSBOND 16 CYS B 76 CYS B 82 1555 1555 2.03 CRYST1 73.832 73.832 53.130 90.00 90.00 120.00 P 65 12 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 0.013544 0.007820 0.000000 0.00000 SCALE2 0.000000 0.015640 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018822 0.00000