HEADER OXYGEN TRANSPORT 07-SEP-92 1LLA TITLE CRYSTAL STRUCTURE OF DEOXYGENATED LIMULUS POLYPHEMUS TITLE 2 SUBUNIT II HEMOCYANIN AT 2.18 ANGSTROMS RESOLUTION: CLUES TITLE 3 FOR A MECHANISM FOR ALLOSTERIC REGULATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOCYANIN (SUBUNIT TYPE II); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LIMULUS POLYPHEMUS; SOURCE 3 ORGANISM_COMMON: ATLANTIC HORSESHOE CRAB; SOURCE 4 ORGANISM_TAXID: 6850 KEYWDS OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR B.HAZES,W.G.J.HOL REVDAT 3 24-FEB-09 1LLA 1 VERSN REVDAT 2 01-APR-03 1LLA 1 JRNL REVDAT 1 31-JAN-94 1LLA 0 JRNL AUTH B.HAZES,K.A.MAGNUS,C.BONAVENTURA,J.BONAVENTURA, JRNL AUTH 2 Z.DAUTER,K.H.KALK,W.G.HOL JRNL TITL CRYSTAL STRUCTURE OF DEOXYGENATED LIMULUS JRNL TITL 2 POLYPHEMUS SUBUNIT II HEMOCYANIN AT 2.18 A JRNL TITL 3 RESOLUTION: CLUES FOR A MECHANISM FOR ALLOSTERIC JRNL TITL 4 REGULATION. JRNL REF PROTEIN SCI. V. 2 597 1993 JRNL REFN ISSN 0961-8368 JRNL PMID 8518732 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.A.MAGNUS,E.E.LATTMAN,A.VOLBEDA,W.G.J.HOL REMARK 1 TITL HEXAMERS OF SUBUNIT II FROM LIMULUS HEMOCYANIN (A REMARK 1 TITL 2 48-MER) HAVE THE SAME QUATERNARY STRUCTURE AS REMARK 1 TITL 3 WHOLE PANULIRUS HEMOCYANIN MOLECULES REMARK 1 REF PROTEINS V. 9 240 1991 REMARK 1 REFN ISSN 0887-3585 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.VOLBEDA,W.G.J.HOL REMARK 1 TITL CRYSTAL STRUCTURE OF HEXAMERIC HAEMOCYANIN FROM REMARK 1 TITL 2 PANULIRUS INTERRUPTUS REFINED AT 3.2 ANGSTROMS REMARK 1 TITL 3 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 209 249 1989 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.NAKASHIMA,P.Q.BEHRENS,M.D.MOORE,E.YOKOTA, REMARK 1 AUTH 2 A.F.RIGGS REMARK 1 TITL STRUCTURE OF HEMOCYANIN II FROM THE HORSHOE CRAB REMARK 1 TITL 2 LIMULUS POLYPHEMUS REMARK 1 REF J.BIOL.CHEM. V. 261 10526 1986 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4860 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 332 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 2.90 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LLA COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. 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 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: R 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 Z,X,Y REMARK 290 3555 Y,Z,X REMARK 290 4555 -Y,-X,-Z REMARK 290 5555 -X,-Z,-Y REMARK 290 6555 -Z,-Y,-X 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 0.499698 0.288617 0.816702 0.00000 REMARK 290 SMTRY2 2 0.866200 -0.166499 -0.471143 0.00000 REMARK 290 SMTRY3 2 0.000000 0.942857 -0.333199 0.00000 REMARK 290 SMTRY1 3 0.499698 0.866200 0.000000 0.00000 REMARK 290 SMTRY2 3 0.288617 -0.166499 0.942857 0.00000 REMARK 290 SMTRY3 3 0.816702 -0.471143 -0.333199 0.00000 REMARK 290 SMTRY1 4 -0.499698 -0.866200 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866200 0.499698 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -0.333199 -0.942857 0.00000 REMARK 290 SMTRY3 5 0.000000 -0.942857 0.333199 0.00000 REMARK 290 SMTRY1 6 -0.499698 -0.288617 -0.816702 0.00000 REMARK 290 SMTRY2 6 -0.288617 -0.833501 0.471143 0.00000 REMARK 290 SMTRY3 6 -0.816702 0.471143 0.333199 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 BASED ON OXYGEN BINDING STUDIES THAT MIMIC THE REMARK 400 CRYSTALLIZATION CONDITIONS THE STRUCTURE IS BELIEVED TO REMARK 400 REPRESENT THE LOW OXYGEN AFFINITY (OR T-STATE) REMARK 400 CONFORMATION. 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 THR A 1 REMARK 465 VAL A 21 REMARK 465 ILE A 22 REMARK 465 GLY A 23 REMARK 465 ASP A 24 REMARK 465 GLY A 25 REMARK 465 ASP A 26 REMARK 465 LYS A 27 REMARK 465 HIS A 28 REMARK 465 LYS A 29 REMARK 465 ALA A 132 REMARK 465 HIS A 133 REMARK 465 VAL A 134 REMARK 465 ARG A 135 REMARK 465 PRO A 136 REMARK 465 GLU A 137 REMARK 465 PHE A 138 REMARK 465 ASP A 139 REMARK 465 GLN A 148 REMARK 465 ASP A 149 REMARK 465 ASN A 527 REMARK 465 GLU A 528 REMARK 465 HIS A 529 REMARK 465 LYS A 530 REMARK 465 ASP A 569 REMARK 465 GLY A 570 REMARK 465 SER A 571 REMARK 465 GLU A 572 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 THR A 20 OG1 CG2 REMARK 470 GLU A 75 CG CD OE1 OE2 REMARK 470 GLU A 140 CG CD OE1 OE2 REMARK 470 SER A 141 OG REMARK 470 PRO A 142 CG CD REMARK 470 ASP A 146 CG OD1 OD2 REMARK 470 VAL A 147 CG1 CG2 REMARK 470 ASN A 152 CG OD1 ND2 REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 GLU A 412 CG CD OE1 OE2 REMARK 470 ARG A 427 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 505 CG CD1 CD2 REMARK 470 LYS A 550 CG CD CE NZ REMARK 470 SER A 573 OG REMARK 470 HIS A 627 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 628 CG CD OE1 OE2 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 NE ARG A 481 O HOH A 940 1.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 3 NE2 HIS A 3 CD2 -0.071 REMARK 500 HIS A 172 NE2 HIS A 172 CD2 -0.072 REMARK 500 HIS A 173 NE2 HIS A 173 CD2 -0.068 REMARK 500 HIS A 239 NE2 HIS A 239 CD2 -0.067 REMARK 500 HIS A 281 NE2 HIS A 281 CD2 -0.073 REMARK 500 HIS A 292 NE2 HIS A 292 CD2 -0.076 REMARK 500 HIS A 299 NE2 HIS A 299 CD2 -0.070 REMARK 500 HIS A 342 NE2 HIS A 342 CD2 -0.068 REMARK 500 HIS A 364 NE2 HIS A 364 CD2 -0.075 REMARK 500 HIS A 419 NE2 HIS A 419 CD2 -0.076 REMARK 500 HIS A 456 NE2 HIS A 456 CD2 -0.067 REMARK 500 HIS A 522 CG HIS A 522 CD2 0.060 REMARK 500 HIS A 555 NE2 HIS A 555 CD2 -0.067 REMARK 500 SER A 610 CA SER A 610 CB 0.100 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 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 58 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 TRP A 65 CD1 - CG - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 TRP A 65 CE2 - CD2 - CG ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 100 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 CYS A 103 CA - CB - SG ANGL. DEV. = -11.8 DEGREES REMARK 500 VAL A 108 CG1 - CB - CG2 ANGL. DEV. = -9.9 DEGREES REMARK 500 TYR A 163 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 TRP A 174 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 TRP A 174 CG - CD2 - CE3 ANGL. DEV. = 5.8 DEGREES REMARK 500 TRP A 176 CD1 - CG - CD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 TRP A 176 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 TRP A 184 CD1 - CG - CD2 ANGL. DEV. = 4.9 DEGREES REMARK 500 TRP A 184 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 195 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 273 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 TRP A 326 CD1 - CG - CD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 TRP A 326 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 340 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 356 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 TRP A 363 CD1 - CG - CD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 TRP A 363 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 411 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 432 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 460 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 480 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 481 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 HIS A 522 CA - C - N ANGL. DEV. = 14.3 DEGREES REMARK 500 HIS A 522 O - C - N ANGL. DEV. = -10.4 DEGREES REMARK 500 TRP A 538 CD1 - CG - CD2 ANGL. DEV. = 4.8 DEGREES REMARK 500 TRP A 538 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES REMARK 500 TRP A 563 CD1 - CG - CD2 ANGL. DEV. = 7.2 DEGREES REMARK 500 TRP A 563 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES REMARK 500 VAL A 580 CB - CA - C ANGL. DEV. = -14.9 DEGREES REMARK 500 TYR A 582 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 THR A 614 N - CA - CB ANGL. DEV. = -12.8 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 SER A 31 134.45 148.10 REMARK 500 SER A 245 -9.17 -146.04 REMARK 500 ASN A 316 85.75 -163.35 REMARK 500 ASN A 322 49.43 -159.89 REMARK 500 ASP A 336 61.42 -150.60 REMARK 500 ASP A 390 -7.43 74.20 REMARK 500 HIS A 522 -141.56 -83.76 REMARK 500 PRO A 591 39.56 -78.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 525 LEU A 526 131.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 222 0.23 SIDE_CHAIN REMARK 500 ARG A 271 0.15 SIDE_CHAIN REMARK 500 ARG A 401 0.27 SIDE_CHAIN REMARK 500 ARG A 411 0.30 SIDE_CHAIN 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 A 966 DISTANCE = 10.05 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 CU A 629 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 173 NE2 REMARK 620 2 HIS A 204 NE2 131.0 REMARK 620 3 HIS A 177 NE2 99.1 125.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 630 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 364 NE2 REMARK 620 2 HIS A 328 NE2 142.1 REMARK 620 3 HIS A 324 NE2 108.4 96.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 631 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 510 O REMARK 620 2 HOH A 889 O 87.6 REMARK 620 3 ASP A 578 O 89.5 166.6 REMARK 620 4 SER A 507 O 114.2 92.4 100.8 REMARK 620 5 ASP A 578 OD1 81.8 89.7 77.0 163.9 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 CU A 629 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 630 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 631 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 632 REMARK 999 REMARK 999 SEQUENCE REMARK 999 REMARK 999 SEQUENCE ADVISORY NOTICE: REMARK 999 THE SEQUENCE HAS BEEN CHANGED IN THREE POSITIONS COMPARED REMARK 999 TO THE PUBLISHED SEQUENCE (NAKASHIMA, 1986). REMARK 999 REMARK 999 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. REMARK 999 REMARK 999 SWISS-PROT ENTRY NAME: HCY2_LIMPO REMARK 999 REMARK 999 SWISS-PROT RESIDUE PDB SEQRES REMARK 999 NAME NUMBER NAME CHAIN SEQ/INSERT CODE REMARK 999 VAL 9 ILE 9 REMARK 999 PHE 408 THR 408 REMARK 999 THR 409 PHE 409 DBREF 1LLA A 1 628 UNP P04253 HCY2_LIMPO 1 628 SEQADV 1LLA ILE A 9 UNP P04253 VAL 9 CONFLICT SEQADV 1LLA THR A 408 UNP P04253 PHE 408 CONFLICT SEQADV 1LLA PHE A 409 UNP P04253 THR 409 CONFLICT SEQRES 1 A 628 THR LEU HIS ASP LYS GLN ILE ARG ILE CYS HIS LEU PHE SEQRES 2 A 628 GLU GLN LEU SER SER ALA THR VAL ILE GLY ASP GLY ASP SEQRES 3 A 628 LYS HIS LYS HIS SER ASP ARG LEU LYS ASN VAL GLY LYS SEQRES 4 A 628 LEU GLN PRO GLY ALA ILE PHE SER CYS PHE HIS PRO ASP SEQRES 5 A 628 HIS LEU GLU GLU ALA ARG HIS LEU TYR GLU VAL PHE TRP SEQRES 6 A 628 GLU ALA GLY ASP PHE ASN ASP PHE ILE GLU ILE ALA LYS SEQRES 7 A 628 GLU ALA ARG THR PHE VAL ASN GLU GLY LEU PHE ALA PHE SEQRES 8 A 628 ALA ALA GLU VAL ALA VAL LEU HIS ARG ASP ASP CYS LYS SEQRES 9 A 628 GLY LEU TYR VAL PRO PRO VAL GLN GLU ILE PHE PRO ASP SEQRES 10 A 628 LYS PHE ILE PRO SER ALA ALA ILE ASN GLU ALA PHE LYS SEQRES 11 A 628 LYS ALA HIS VAL ARG PRO GLU PHE ASP GLU SER PRO ILE SEQRES 12 A 628 LEU VAL ASP VAL GLN ASP THR GLY ASN ILE LEU ASP PRO SEQRES 13 A 628 GLU TYR ARG LEU ALA TYR TYR ARG GLU ASP VAL GLY ILE SEQRES 14 A 628 ASN ALA HIS HIS TRP HIS TRP HIS LEU VAL TYR PRO SER SEQRES 15 A 628 THR TRP ASN PRO LYS TYR PHE GLY LYS LYS LYS ASP ARG SEQRES 16 A 628 LYS GLY GLU LEU PHE TYR TYR MET HIS GLN GLN MET CYS SEQRES 17 A 628 ALA ARG TYR ASP CYS GLU ARG LEU SER ASN GLY MET HIS SEQRES 18 A 628 ARG MET LEU PRO PHE ASN ASN PHE ASP GLU PRO LEU ALA SEQRES 19 A 628 GLY TYR ALA PRO HIS LEU THR HIS VAL ALA SER GLY LYS SEQRES 20 A 628 TYR TYR SER PRO ARG PRO ASP GLY LEU LYS LEU ARG ASP SEQRES 21 A 628 LEU GLY ASP ILE GLU ILE SER GLU MET VAL ARG MET ARG SEQRES 22 A 628 GLU ARG ILE LEU ASP SER ILE HIS LEU GLY TYR VAL ILE SEQRES 23 A 628 SER GLU ASP GLY SER HIS LYS THR LEU ASP GLU LEU HIS SEQRES 24 A 628 GLY THR ASP ILE LEU GLY ALA LEU VAL GLU SER SER TYR SEQRES 25 A 628 GLU SER VAL ASN HIS GLU TYR TYR GLY ASN LEU HIS ASN SEQRES 26 A 628 TRP GLY HIS VAL THR MET ALA ARG ILE HIS ASP PRO ASP SEQRES 27 A 628 GLY ARG PHE HIS GLU GLU PRO GLY VAL MET SER ASP THR SEQRES 28 A 628 SER THR SER LEU ARG ASP PRO ILE PHE TYR ASN TRP HIS SEQRES 29 A 628 ARG PHE ILE ASP ASN ILE PHE HIS GLU TYR LYS ASN THR SEQRES 30 A 628 LEU LYS PRO TYR ASP HIS ASP VAL LEU ASN PHE PRO ASP SEQRES 31 A 628 ILE GLN VAL GLN ASP VAL THR LEU HIS ALA ARG VAL ASP SEQRES 32 A 628 ASN VAL VAL HIS THR PHE MET ARG GLU GLN GLU LEU GLU SEQRES 33 A 628 LEU LYS HIS GLY ILE ASN PRO GLY ASN ALA ARG SER ILE SEQRES 34 A 628 LYS ALA ARG TYR TYR HIS LEU ASP HIS GLU PRO PHE SER SEQRES 35 A 628 TYR ALA VAL ASN VAL GLN ASN ASN SER ALA SER ASP LYS SEQRES 36 A 628 HIS ALA THR VAL ARG ILE PHE LEU ALA PRO LYS TYR ASP SEQRES 37 A 628 GLU LEU GLY ASN GLU ILE LYS ALA ASP GLU LEU ARG ARG SEQRES 38 A 628 THR ALA ILE GLU LEU ASP LYS PHE LYS THR ASP LEU HIS SEQRES 39 A 628 PRO GLY LYS ASN THR VAL VAL ARG HIS SER LEU ASP SER SEQRES 40 A 628 SER VAL THR LEU SER HIS GLN PRO THR PHE GLU ASP LEU SEQRES 41 A 628 LEU HIS GLY VAL GLY LEU ASN GLU HIS LYS SER GLU TYR SEQRES 42 A 628 CYS SER CYS GLY TRP PRO SER HIS LEU LEU VAL PRO LYS SEQRES 43 A 628 GLY ASN ILE LYS GLY MET GLU TYR HIS LEU PHE VAL MET SEQRES 44 A 628 LEU THR ASP TRP ASP LYS ASP LYS VAL ASP GLY SER GLU SEQRES 45 A 628 SER VAL ALA CYS VAL ASP ALA VAL SER TYR CYS GLY ALA SEQRES 46 A 628 ARG ASP HIS LYS TYR PRO ASP LYS LYS PRO MET GLY PHE SEQRES 47 A 628 PRO PHE ASP ARG PRO ILE HIS THR GLU HIS ILE SER ASP SEQRES 48 A 628 PHE LEU THR ASN ASN MET PHE ILE LYS ASP ILE LYS ILE SEQRES 49 A 628 LYS PHE HIS GLU HET CU A 629 1 HET CU A 630 1 HET NA A 631 1 HET CL A 632 1 HETNAM CU COPPER (II) ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 CU 2(CU 2+) FORMUL 4 NA NA 1+ FORMUL 5 CL CL 1- FORMUL 6 HOH *332(H2 O) HELIX 1 1 LEU A 2 GLU A 14 1 13 HELIX 2 2 GLN A 15 ALA A 19 5 5 HELIX 3 3 ASP A 32 VAL A 37 5 6 HELIX 4 4 HIS A 50 GLU A 66 1 17 HELIX 5 5 ASP A 69 ARG A 81 1 13 HELIX 6 6 ASN A 85 ARG A 100 1 16 HELIX 7 7 ASP A 101 LYS A 104 5 4 HELIX 8 8 PRO A 110 PHE A 115 1 6 HELIX 9 9 PRO A 116 PHE A 119 5 4 HELIX 10 10 PRO A 121 LYS A 131 1 11 HELIX 11 11 ASP A 155 ARG A 159 5 5 HELIX 12 12 LEU A 160 GLU A 165 1 6 HELIX 13 13 ASP A 166 TYR A 180 1 15 HELIX 14 14 ASN A 185 GLY A 190 1 6 HELIX 15 15 ARG A 195 ASN A 218 1 24 HELIX 16 16 GLU A 265 GLY A 283 1 19 HELIX 17 17 HIS A 299 SER A 310 1 12 HELIX 18 18 ASN A 316 GLY A 321 1 6 HELIX 19 19 ASN A 322 ARG A 333 1 12 HELIX 20 20 GLY A 346 ASP A 350 5 5 HELIX 21 21 THR A 353 ARG A 356 5 4 HELIX 22 22 ASP A 357 ASN A 376 1 20 HELIX 23 23 ASP A 382 ASN A 387 1 6 HELIX 24 24 LYS A 475 ALA A 483 1 9 HELIX 25 25 LEU A 505 SER A 507 5 3 HELIX 26 26 THR A 516 HIS A 522 1 7 HELIX 27 27 HIS A 541 LEU A 543 5 3 HELIX 28 28 TRP A 563 LYS A 567 1 5 HELIX 29 29 ALA A 579 GLY A 584 1 6 HELIX 30 30 HIS A 608 PHE A 612 5 5 SHEET 1 A 7 ILE A 143 ASP A 146 0 SHEET 2 A 7 ILE A 429 HIS A 438 1 O LYS A 430 N VAL A 145 SHEET 3 A 7 VAL A 405 GLU A 416 -1 N PHE A 409 O ASP A 437 SHEET 4 A 7 MET A 617 PHE A 626 1 O LYS A 623 N VAL A 406 SHEET 5 A 7 MET A 552 ASP A 562 -1 N MET A 552 O ILE A 624 SHEET 6 A 7 LYS A 455 PRO A 465 -1 O THR A 458 N THR A 561 SHEET 7 A 7 ILE A 484 LEU A 493 -1 N ILE A 484 O LEU A 463 SHEET 1 B 2 TYR A 284 ILE A 286 0 SHEET 2 B 2 HIS A 292 THR A 294 -1 O LYS A 293 N VAL A 285 SHEET 1 C 3 ILE A 391 HIS A 399 0 SHEET 2 C 3 SER A 442 ASN A 449 -1 O SER A 442 N HIS A 399 SHEET 3 C 3 GLY A 496 HIS A 503 -1 N GLY A 496 O ASN A 449 SHEET 1 D 2 THR A 510 LEU A 511 0 SHEET 2 D 2 TRP A 538 PRO A 539 1 O TRP A 538 N LEU A 511 SSBOND 1 CYS A 534 CYS A 576 1555 1555 2.00 SSBOND 2 CYS A 536 CYS A 583 1555 1555 2.00 LINK CU CU A 629 NE2 HIS A 173 1555 1555 2.10 LINK CU CU A 629 NE2 HIS A 204 1555 1555 1.94 LINK CU CU A 629 NE2 HIS A 177 1555 1555 2.01 LINK CU CU A 630 NE2 HIS A 364 1555 1555 1.92 LINK CU CU A 630 NE2 HIS A 328 1555 1555 2.08 LINK CU CU A 630 NE2 HIS A 324 1555 1555 2.17 LINK NA NA A 631 O THR A 510 1555 1555 2.35 LINK NA NA A 631 O HOH A 889 1555 1555 2.43 LINK NA NA A 631 O ASP A 578 1555 1555 2.31 LINK NA NA A 631 O SER A 507 1555 1555 2.29 LINK OD1 ASP A 578 NA NA A 631 1555 1555 2.79 CISPEP 1 GLU A 309 SER A 310 0 -12.04 CISPEP 2 PHE A 598 PRO A 599 0 1.16 SITE 1 AC1 3 HIS A 173 HIS A 177 HIS A 204 SITE 1 AC2 3 HIS A 324 HIS A 328 HIS A 364 SITE 1 AC3 6 SER A 507 THR A 510 SER A 512 ASP A 578 SITE 2 AC3 6 HOH A 875 HOH A 889 SITE 1 AC4 3 SER A 47 ARG A 333 SER A 349 CRYST1 117.002 117.002 117.002 60.02 60.02 60.02 R 3 2 6 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 0.008547 -0.004931 -0.003487 0.00000 SCALE2 0.000000 0.009867 -0.003487 0.00000 SCALE3 0.000000 0.000000 0.010465 0.00000