HEADER HORMONE 06-DEC-04 2BF9 TITLE ANISOTROPIC REFINEMENT OF AVIAN (TURKEY) PANCREATIC POLYPEPTIDE AT 0. TITLE 2 99 ANGSTROMS RESOLUTION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PANCREATIC HORMONE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AVIAN PANCREATIC POLYPEPTIDE, PP, PANCREATIC POLYPEPTIDE; COMPND 5 OTHER_DETAILS: COMPLEX WITH ZN(II) ION. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MELEAGRIS GALLOPAVO; SOURCE 3 ORGANISM_COMMON: DOMESTIC TURKEY; SOURCE 4 ORGANISM_TAXID: 9103; SOURCE 5 ORGAN: PANCREAS; SOURCE 6 CELL: ISLETS OF LANGERHANS; SOURCE 7 OTHER_DETAILS: COLLECTED FROM COMMERCIAL UK TURKEY FARM. KEYWDS HORMONE, PANCREATIC HORMONE, TURKEY, PANCREAS, POLYPEPTIDE, ATOMIC KEYWDS 2 RESOLUTION, ANISOTROPIC REFINEMENT EXPDTA X-RAY DIFFRACTION AUTHOR I.TICKLE,I.GLOVER,J.PITTS,S.WOOD,T.L.BLUNDELL REVDAT 4 22-MAY-19 2BF9 1 REMARK LINK REVDAT 3 24-FEB-09 2BF9 1 VERSN REVDAT 2 19-SEP-06 2BF9 1 SEQRES REVDAT 1 08-DEC-04 2BF9 0 JRNL AUTH I.GLOVER,I.HANEEF,J.PITTS,S.WOOD,D.MOSS,I.TICKLE, JRNL AUTH 2 T.L.BLUNDELL JRNL TITL CONFORMATIONAL FLEXIBILITY IN A SMALL GLOBULAR HORMONE. JRNL TITL 2 X-RAY ANALYSIS OF AVIAN PANCREATIC POLYPEPTIDE AT 0.98 JRNL TITL 3 ANGSTROMS RESOLUTION JRNL REF BIOPOLYMERS V. 22 293 1983 JRNL REFN ISSN 0006-3525 JRNL PMID 6673760 JRNL DOI 10.1002/BIP.360220138 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.E.PITTS,I.J.TICKLE,S.P.WOOD,T.L.BLUNDELL REMARK 1 TITL CRYSTAL STRUCTURE ANALYSIS OF AVIAN PANCREATIC POLYPEPTIDE REMARK 1 TITL 2 AT 1.37 ANGSTROMS RESOLUTION REMARK 1 REF KRISTALLOGRAFIYA V. 27 97 1982 REMARK 1 REFN ISSN 0023-4761 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.E.PITTS,I.J.TICKLE,S.P.WOOD,T.L.BLUNDELL REMARK 1 TITL CRYSTAL STRUCTURE ANALYSIS OF AVIAN PANCREATIC POLYPEPTIDE REMARK 1 TITL 2 AT 1.37 ANGSTROMS RESOLUTION REMARK 1 REF SOV.PHYS.CRYSTALLOGR.(ENGL. V. 27 56 1982 REMARK 1 REF 2 TRANSL.) REMARK 1 REFN ISSN 0038-5638 REMARK 1 REFERENCE 3 REMARK 1 AUTH T.L.BLUNDELL,J.E.PITTS,I.J.TICKLE,S.P.WOOD,C.-W.WU REMARK 1 TITL X-RAY ANALYSIS (1.4-ANGSTROMS RESOLUTION) OF AVIAN REMARK 1 TITL 2 PANCREATIC POLYPEPTIDE. SMALL GLOBULAR PROTEIN HORMONE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 78 4175 1981 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 16593056 REMARK 1 DOI 10.1073/PNAS.78.7.4175 REMARK 1 REFERENCE 4 REMARK 1 AUTH S.P.WOOD,J.E.PITTS,T.L.BLUNDELL,I.J.TICKLE,J.A.JENKINS REMARK 1 TITL PURIFICATION, CRYSTALLISATION AND PRELIMINARY X-RAY STUDIES REMARK 1 TITL 2 ON AVIAN PANCREATIC POLYPEPTIDE REMARK 1 REF EUR.J.BIOCHEM. V. 78 119 1977 REMARK 1 REFN ISSN 0014-2956 REMARK 1 PMID 913391 REMARK 1 DOI 10.1111/J.1432-1033.1977.TB11720.X REMARK 1 REFERENCE 5 REMARK 1 AUTH J.R.KIMMEL,L.J.HAYDEN,H.G.POLLOCK REMARK 1 TITL ISOLATION AND CHARACTERIZATION OF A NEW PANCREATIC REMARK 1 TITL 2 POLYPEPTIDE HORMONE REMARK 1 REF J.BIOL.CHEM. V. 250 9369 1975 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 1194289 REMARK 2 REMARK 2 RESOLUTION. 0.99 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) : 0.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE 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) : 0.137 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.137 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 852 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 17058 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.098 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.098 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.137 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 567 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 11550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 301 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 382.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 281.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3457 REMARK 3 NUMBER OF RESTRAINTS : 1694 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.026 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.020 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.093 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.082 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.013 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.007 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.000 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THIS IS A REFINEMENT OF PDB ENTRY 1PPT REMARK 3 USING NEW X-RAY DATA AT ATOMIC RESOLUTION. REMARK 4 REMARK 4 2BF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1290021858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-83 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 4 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : HILGER-WATTS 1.2KW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : HELIUM PATH REMARK 200 REMARK 200 DETECTOR TYPE : Y290 SCINTILLATION COUNTER REMARK 200 DETECTOR MANUFACTURER : HILGER-WATTS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ON-LINE CENTROID INTEGRATION REMARK 200 DATA SCALING SOFTWARE : HRS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17058 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.990 REMARK 200 RESOLUTION RANGE LOW (A) : 27.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS 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 (%): 31.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5MG/ML POLYPEPTIDE IN 0.1M TRIS-HCL REMARK 280 BUFFER, 0.001M ZN(OAC)2, PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 17.09000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.46000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 17.09000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.46000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2004 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2032 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2048 LIES ON A SPECIAL POSITION. 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 19 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 19 NE - CZ - NH2 ANGL. DEV. = -3.4 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 ARG A 35 56.10 -91.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2005 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A2036 DISTANCE = 5.81 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 37 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 1 N REMARK 620 2 ASP A 23 OD2 133.2 REMARK 620 3 HIS A 34 NE2 121.4 104.9 REMARK 620 4 HOH A2082 O 90.0 95.6 91.8 REMARK 620 5 GLY A 1 O 78.2 91.5 95.5 168.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 37 DBREF 2BF9 A 1 36 UNP P68249 PAHO_MELGA 1 36 SEQRES 1 A 36 GLY PRO SER GLN PRO THR TYR PRO GLY ASP ASP ALA PRO SEQRES 2 A 36 VAL GLU ASP LEU ILE ARG PHE TYR ASN ASP LEU GLN GLN SEQRES 3 A 36 TYR LEU ASN VAL VAL THR ARG HIS ARG TYC HET TYC A 36 24 HET ZN A 37 1 HETNAM TYC L-TYROSINAMIDE HETNAM ZN ZINC ION FORMUL 1 TYC C9 H12 N2 O2 FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *82(H2 O) HELIX 1 1 PRO A 13 THR A 32 1 20 LINK C ARG A 35 N TYC A 36 1555 1555 1.32 LINK ZN ZN A 37 N GLY A 1 1555 1555 2.04 LINK ZN ZN A 37 OD2 ASP A 23 1555 2556 1.98 LINK ZN ZN A 37 NE2 HIS A 34 1555 4546 2.01 LINK ZN ZN A 37 O HOH A2082 1555 1555 2.14 LINK ZN ZN A 37 O GLY A 1 1555 1555 2.20 SITE 1 AC1 4 GLY A 1 ASP A 23 HIS A 34 HOH A2082 CRYST1 34.180 32.920 28.450 90.00 105.26 90.00 C 1 2 1 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 0.029257 0.000000 0.007982 0.00000 SCALE2 0.000000 0.030377 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036434 0.00000