PDB Short entry for 1XY1 HEADER HORMONE 05-JUN-87 1XY1 TITLE CRYSTAL STRUCTURE ANALYSIS OF DEAMINO-OXYTOCIN. CONFORMATIONAL TITLE 2 FLEXIBILITY AND RECEPTOR BINDING COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-MERCAPTOPROPIONATE-OXYTOCIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS HORMONE EXPDTA X-RAY DIFFRACTION AUTHOR J.HUSAIN,T.L.BLUNDELL,S.P.WOOD,I.J.TICKLE,S.COOPER,J.E.PITTS REVDAT 7 29-NOV-17 1XY1 1 HELIX REVDAT 6 29-FEB-12 1XY1 1 JRNL VERSN REVDAT 5 24-FEB-09 1XY1 1 VERSN REVDAT 4 01-APR-03 1XY1 1 JRNL REVDAT 3 15-OCT-90 1XY1 3 REMARK HET HETATM ANISOU REVDAT 2 09-OCT-88 1XY1 1 REMARK REVDAT 1 16-APR-88 1XY1 0 JRNL AUTH S.P.WOOD,I.J.TICKLE,A.M.TREHARNE,J.E.PITTS,Y.MASCARENHAS, JRNL AUTH 2 J.Y.LI,J.HUSAIN,S.COOPER,T.L.BLUNDELL,V.J.HRUBY,A.BUKU, JRNL AUTH 3 A.J.FISCHMAN,H.R.WYSSBROD JRNL TITL CRYSTAL STRUCTURE ANALYSIS OF DEAMINO-OXYTOCIN: JRNL TITL 2 CONFORMATIONAL FLEXIBILITY AND RECEPTOR BINDING. JRNL REF SCIENCE V. 232 633 1986 JRNL REFN ISSN 0036-8075 JRNL PMID 3008332 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.E.PITTS,S.P.WOOD,I.J.TICKLE,A.M.TREHARNE,Y.MASCARENHAS, REMARK 1 AUTH 2 J.Y.LI,J.HUSAIN,S.COOPER,T.L.BLUNDELL,V.J.HRUBY, REMARK 1 AUTH 3 H.R.WYSSBROD,A.BAKU,A.J.FISCHMAN REMARK 1 TITL X-RAY ANALYSIS OF DEAMINO-OXYTOCIN. CONFORMATIONAL REMARK 1 TITL 2 FLEXIBILITY AND RECEPTOR BINDING REMARK 1 EDIT R.M.BURNETT, H.J.VOGEL REMARK 1 REF BIOLOGICAL ORGANIZATION. 289 1987 REMARK 1 REF 2 MACROMOLECULAR INTERACTIONS REMARK 1 REF 3 AT HIGH RESOLUTION REMARK 1 PUBL ACADEMIC PRESS, ORLANDO,FL REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH A.M.TREHARNE,S.P.WOOD,I.J.TICKLE,J.E.PITTS,J.HUSAIN, REMARK 1 AUTH 2 I.D.GLOVER,S.COOPER,T.L.BLUNDELL REMARK 1 TITL X-RAY ANALYSIS OF POLYPEPTIDE HORMONES AT (LESS THAN OR REMARK 1 TITL 2 EQUAL) 1 ANGSTROM RESOLUTION. ANISOTROPIC THERMAL MOTION AND REMARK 1 TITL 3 SECONDARY STRUCTURE OF PANCREATIC POLYPEPTIDE AND REMARK 1 TITL 4 DEAMINO-OXYTOCIN REMARK 1 EDIT D.MORAS, J.DRENTH, B.STRANDBERG, D.SUCK, K.WILSON REMARK 1 REF CRYSTALLOGRAPHY IN MOLECULAR V. 126 153 1988 REMARK 1 REF 2 BIOLOGY REMARK 1 PUBL PLENUM, NEW YORK, NY REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX-76 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL 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)) : 0.088 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)) : 4681 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 136 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 13 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) : NULL 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 : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XY1 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_1000177325. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 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: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 4.52000 REMARK 290 SMTRY3 2 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 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 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 A 5 74.51 -150.42 REMARK 500 ASN B 5 65.24 -157.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 10 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 B 10 DBREF 1XY1 A 1 10 PDB 1XY1 1XY1 1 10 DBREF 1XY1 B 1 10 PDB 1XY1 1XY1 1 10 SEQRES 1 A 10 MPT TYR ILE GLN ASN CYS PRO LEU GLY NH2 SEQRES 1 B 10 MPT TYR ILE GLN ASN CYS PRO LEU GLY NH2 HET MPT A 1 10 HET NH2 A 10 3 HET MPT B 1 10 HET NH2 B 10 3 HETNAM MPT BETA-MERCAPTOPROPIONIC ACID HETNAM NH2 AMINO GROUP FORMUL 1 MPT 2(C3 H6 O2 S) FORMUL 1 NH2 2(H2 N) FORMUL 3 HOH *13(H2 O) LINK SG AMPT A 1 SG CYS A 6 1555 1555 1.95 LINK SG BMPT A 1 SG CYS A 6 1555 1555 2.10 LINK SG AMPT B 1 SG CYS B 6 1555 1555 2.08 LINK SG BMPT B 1 SG CYS B 6 1555 1555 1.95 LINK C GLY A 9 N NH2 A 10 1555 1555 1.42 LINK C GLY B 9 N NH2 B 10 1555 1555 1.39 LINK C MPT A 1 N TYR A 2 1555 1555 1.40 LINK C MPT B 1 N TYR B 2 1555 1555 1.41 SITE 1 AC1 2 GLY A 9 HOH A 11 SITE 1 AC2 2 GLY B 9 HOH B 13 CRYST1 27.270 9.040 23.040 90.00 102.24 90.00 P 1 21 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 0.036670 0.000000 0.007950 0.00000 SCALE2 0.000000 0.110619 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044410 0.00000 MTRIX1 1 -0.997700 -0.066200 0.010900 0.03300 1 MTRIX2 1 -0.065200 0.995100 0.074500 0.02000 1 MTRIX3 1 -0.015800 0.074500 -0.997200 -0.00600 1 HETATM 1 CA MPT A 1 19.392 5.714 9.147 1.00 0.07 C ANISOU 1 CA MPT A 1 696 696 696 0 0 0 C HETATM 2 C MPT A 1 18.131 5.091 8.587 1.00 0.06 C ANISOU 2 C MPT A 1 464 754 446 154 63 -64 C HETATM 3 O MPT A 1 17.488 4.191 9.060 1.00 0.08 O ANISOU 3 O MPT A 1 793 964 515 -93 -23 11 O HETATM 4 CB MPT A 1 20.530 4.821 9.169 1.00 0.22 C ANISOU 4 CB MPT A 1 2165 2165 2165 0 0 0 C HETATM 5 SG AMPT A 1 22.103 5.593 8.460 0.66 0.07 S ANISOU 5 SG AMPT A 1 537 827 716 -77 83 -38 S HETATM 6 SG BMPT A 1 21.289 4.124 7.744 0.34 0.25 S ANISOU 6 SG BMPT A 1 3519 1848 2169 -911 -985 -602 S HETATM 7 HA1 MPT A 1 19.191 6.034 10.159 1.00 0.49 H ANISOU 7 HA1 MPT A 1 4850 4850 4850 0 0 0 H HETATM 8 HA2 MPT A 1 19.644 6.572 8.541 1.00 0.04 H ANISOU 8 HA2 MPT A 1 358 358 358 0 0 0 H HETATM 9 HB1 MPT A 1 21.313 5.364 9.677 1.00 1.15 H ANISOU 9 HB1 MPT A 1 11540 11540 11540 0 0 0 H HETATM 10 HB2 MPT A 1 20.225 3.980 9.775 1.00 1.00 H ANISOU 10 HB2 MPT A 1 10034 10034 10034 0 0 0 H