PDB Short entry for 1DZB HEADER IMMUNE SYSTEM 23-FEB-00 1DZB TITLE CRYSTAL STRUCTURE OF PHAGE LIBRARY-DERIVED SINGLE-CHAIN FV FRAGMENT TITLE 2 1F9 IN COMPLEX WITH TURKEY EGG-WHITE LYSOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCFV FRAGMENT 1F9; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SEE REMARK 400; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TURKEY EGG-WHITE LYSOZYME C; COMPND 7 CHAIN: X, Y; COMPND 8 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C; COMPND 9 EC: 3.2.1.17 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: MELEAGRIS GALLOPAVO; SOURCE 7 ORGANISM_COMMON: COMMON TURKEY; SOURCE 8 ORGANISM_TAXID: 9103 KEYWDS IMMUNE SYSTEM, COMPLEX (ANTIBODY ANTIGEN), SINGLE-DOMAIN ANTIBODY, KEYWDS 2 TURKEY EGG-WHITE LYSOZYME, ANTIBODY- PROTEIN COMPLEX, SINGLE-CHAIN KEYWDS 3 FV FRAGMENT EXPDTA X-RAY DIFFRACTION AUTHOR J.AY,T.KEITEL,G.KUETTNER,H.WESSNER,C.SCHOLZ,M.HAHN,W.HOEHNE REVDAT 4 06-DEC-23 1DZB 1 REMARK REVDAT 3 24-JUL-19 1DZB 1 REMARK REVDAT 2 24-FEB-09 1DZB 1 VERSN REVDAT 1 02-NOV-00 1DZB 0 JRNL AUTH J.AY,T.KEITEL,G.KUTTNER,H.WESSNER,C.SCHOLZ,M.HAHN,W.HOHNE JRNL TITL CRYSTAL STRUCTURE OF A PHAGE LIBRARY-DERIVED SINGLE-CHAIN FV JRNL TITL 2 FRAGMENT COMPLEXED WITH TURKEY EGG -WHITE LYSOZYME AT 2.0 A JRNL TITL 3 RESOLUTION JRNL REF J.MOL.BIOL. V. 301 239 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10926506 JRNL DOI 10.1006/JMBI.2000.3971 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.KUTTNER,T.KEITEL,E.GIESSMANN,H.WESSNER,C.SCHOLZ REMARK 1 TITL A PHAGE LIBRARY-DERIVED SINGLE-CHAIN FV FRAGMENT IN COMPLEX REMARK 1 TITL 2 WITH A PHAGE LIBRARY-DERIVED SINGLE-CHAIN FV FRAGMENT IN REMARK 1 TITL 3 COMPLEX WITHTURKEY EGG-WHITE LYSOZYME: CHARACTERIZATION, REMARK 1 TITL 4 CRYSTALLIZATION ANDPRELIMINARY X-RAY ANALYSIS REMARK 1 REF MOL.IMMUNOL. V. 35 189 1998 REMARK 1 REFN ISSN 0161-5890 REMARK 1 PMID 9694519 REMARK 1 DOI 10.1016/S0161-5890(98)00027-3 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 3 NUMBER OF REFLECTIONS : 40205 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5442 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.30 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.015 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.045 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.083 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 10.600; 7.000 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.166 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.194 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.264 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.165 ; 0.300 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; 15.000 REMARK 3 PLANAR (DEGREES) : 10.600; 7.000 REMARK 3 STAGGERED (DEGREES) : 21.300; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 28.100; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.719 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.025 ; 4.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.923 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.209 ; 4.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THERE ARE TWO MOLECULES PER ASYMMETRIC REMARK 3 UNIT REMARK 4 REMARK 4 1DZB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1290004622. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.00 REMARK 200 NUMBER OF CRYSTALS USED : 5 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.04500 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 : 40240 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.13900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.770 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1JHL REMARK 200 REMARK 200 REMARK: THERE ARE TWO MOLECULE COMPLEXES PER ASYMMETRIC UNIT REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A SOLUTION OF SCFV FRAGMENT 1F9/TEL REMARK 280 COMPLEX IN A 1:1 RATION IN 5 MM TRIS/HCL PH 7.5, 0.1 M NACL WAS REMARK 280 MIXED WITH 10% PEG4000, 0.1 M AMMONIUMACETAT AND 0.05 M REMARK 280 SODIUMACETATE BUFFER PH 5.0 AND EQUILIBRATED AGAINST 30% PEG4000, REMARK 280 PH 5.00 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 56.22000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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, X 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 REMARK 350 BIOMOLECULE: 2 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: B, Y 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 CHAIN A,B: REMARK 400 EACH CHAIN IS MADE UP FROM: REMARK 400 REMARK 400 RESIDUES 1-116: HEAVY CHAIN VARIABLE REGION OF 1F9 REMARK 400 RESIDUES 117-131: GGGGSGGGGSGGGGS LINKER REMARK 400 RESIDUES 201-307: LIGHT CHAIN VARIABLE REGION OF 1F9 REMARK 400 RESIDUES 308-311: RAAA LINKER TO MYC TAG REMARK 400 RESIDUES 312-322: EQKLISEEDLN MYC TAG REMARK 400 REMARK 400 THERE IS NO ELECTRON DENSITY FOUND FOR THE LINKERPEPTIDE REMARK 400 (GGGGS)3 BETWEEN THE HEAVY CHAIN VARIABLE REGION AND THE REMARK 400 LIGHT CHAIN VARIABLE REGION OF THE SCFV FRAGMENT. NO REMARK 400 ELECTRON DENSITY WAS OBSERVED FOR THE LAST RESIDUE OF REMARK 400 C-TERMINUS OF VL LYS-107 AND FOR THE FOUR RESIDUES REMARK 400 (ARG-(ALA)3) CONNECTING THE C-TERMINUS OF VL AND THE REMARK 400 MYC-TAG. FOR THE MYC-TAG IS ALSO NO ELECTRON DENSITY REMARK 400 VISIBLE. 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 118 REMARK 465 GLY A 119 REMARK 465 GLY A 120 REMARK 465 SER A 121 REMARK 465 GLY A 122 REMARK 465 GLY A 123 REMARK 465 GLY A 124 REMARK 465 GLY A 125 REMARK 465 SER A 126 REMARK 465 GLY A 127 REMARK 465 GLY A 128 REMARK 465 GLY A 129 REMARK 465 GLY A 130 REMARK 465 SER A 131 REMARK 465 ARG A 308 REMARK 465 ALA A 309 REMARK 465 ALA A 310 REMARK 465 ALA A 311 REMARK 465 GLU A 312 REMARK 465 GLN A 313 REMARK 465 LYS A 314 REMARK 465 LEU A 315 REMARK 465 ILE A 316 REMARK 465 SER A 317 REMARK 465 GLU A 318 REMARK 465 GLU A 319 REMARK 465 ASP A 320 REMARK 465 LEU A 321 REMARK 465 ASN A 322 REMARK 465 GLY B 118 REMARK 465 GLY B 119 REMARK 465 GLY B 120 REMARK 465 SER B 121 REMARK 465 GLY B 122 REMARK 465 GLY B 123 REMARK 465 GLY B 124 REMARK 465 GLY B 125 REMARK 465 SER B 126 REMARK 465 GLY B 127 REMARK 465 GLY B 128 REMARK 465 GLY B 129 REMARK 465 GLY B 130 REMARK 465 SER B 131 REMARK 465 ARG B 308 REMARK 465 ALA B 309 REMARK 465 ALA B 310 REMARK 465 ALA B 311 REMARK 465 GLU B 312 REMARK 465 GLN B 313 REMARK 465 LYS B 314 REMARK 465 LEU B 315 REMARK 465 ILE B 316 REMARK 465 SER B 317 REMARK 465 GLU B 318 REMARK 465 GLU B 319 REMARK 465 ASP B 320 REMARK 465 LEU B 321 REMARK 465 ASN B 322 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 GLY A 117 CA C O REMARK 470 LYS A 307 CA C O CB CG CD CE REMARK 470 LYS A 307 NZ REMARK 470 GLY B 117 CA C O REMARK 470 LYS B 307 CA C O CB CG CD CE REMARK 470 LYS B 307 NZ 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 ASN X 74 N ASN X 74 CA 0.128 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 GLY A 8 N - CA - C ANGL. DEV. = 32.4 DEGREES REMARK 500 LEU A 81 CB - CG - CD2 ANGL. DEV. = 17.0 DEGREES REMARK 500 ARG A 98 CD - NE - CZ ANGL. DEV. = 10.1 DEGREES REMARK 500 TRP A 99 N - CA - CB ANGL. DEV. = 14.0 DEGREES REMARK 500 TRP A 99 CA - CB - CG ANGL. DEV. = 17.2 DEGREES REMARK 500 TYR A 102 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 104 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 THR A 110 CA - CB - CG2 ANGL. DEV. = 9.1 DEGREES REMARK 500 SER A 207 CA - C - O ANGL. DEV. = -26.0 DEGREES REMARK 500 SER A 207 O - C - N ANGL. DEV. = 15.3 DEGREES REMARK 500 PRO A 208 CA - N - CD ANGL. DEV. = -15.7 DEGREES REMARK 500 PRO A 208 N - CA - CB ANGL. DEV. = 10.4 DEGREES REMARK 500 LEU A 215 C - N - CA ANGL. DEV. = 19.2 DEGREES REMARK 500 LEU A 215 CB - CG - CD1 ANGL. DEV. = 12.8 DEGREES REMARK 500 GLN A 227 C - N - CA ANGL. DEV. = 17.1 DEGREES REMARK 500 ILE A 229 N - CA - CB ANGL. DEV. = 15.0 DEGREES REMARK 500 SER A 231 N - CA - CB ANGL. DEV. = -9.9 DEGREES REMARK 500 ARG A 234 CG - CD - NE ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG A 234 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 LYS A 239 CA - CB - CG ANGL. DEV. = 17.2 DEGREES REMARK 500 LEU A 273 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 ASP A 281 CA - CB - CG ANGL. DEV. = 29.9 DEGREES REMARK 500 TYR A 287 CB - CG - CD2 ANGL. DEV. = 4.4 DEGREES REMARK 500 TYR A 287 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 SER A 294 CA - C - O ANGL. DEV. = -28.1 DEGREES REMARK 500 PRO A 295 CA - N - CD ANGL. DEV. = -12.4 DEGREES REMARK 500 PRO A 295 N - CA - CB ANGL. DEV. = 13.2 DEGREES REMARK 500 PRO A 295 N - CD - CG ANGL. DEV. = 12.6 DEGREES REMARK 500 GLY B 8 O - C - N ANGL. DEV. = -11.3 DEGREES REMARK 500 ALA B 9 C - N - CA ANGL. DEV. = 16.2 DEGREES REMARK 500 ALA B 9 N - CA - CB ANGL. DEV. = 11.6 DEGREES REMARK 500 ASP B 31 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 GLU B 42 CA - CB - CG ANGL. DEV. = 18.9 DEGREES REMARK 500 ILE B 48 CA - CB - CG2 ANGL. DEV. = 15.8 DEGREES REMARK 500 ARG B 50 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 TYR B 60 CB - CA - C ANGL. DEV. = -12.1 DEGREES REMARK 500 LYS B 63 CA - CB - CG ANGL. DEV. = 17.5 DEGREES REMARK 500 ASP B 90 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG B 98 CD - NE - CZ ANGL. DEV. = 26.6 DEGREES REMARK 500 ARG B 98 NH1 - CZ - NH2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ARG B 98 NE - CZ - NH1 ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG B 98 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP B 100 CA - CB - CG ANGL. DEV. = 16.4 DEGREES REMARK 500 ASP B 100 OD1 - CG - OD2 ANGL. DEV. = -11.7 DEGREES REMARK 500 ASP B 100 CB - CG - OD1 ANGL. DEV. = 11.0 DEGREES REMARK 500 TYR B 102 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 TYR B 102 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ASP B 201 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 SER B 207 CA - C - O ANGL. DEV. = -24.6 DEGREES REMARK 500 PRO B 208 CA - N - CD ANGL. DEV. = -12.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 92 ANGLE DEVIATIONS. 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 ILE A 48 -60.04 -90.90 REMARK 500 TRP A 101 123.63 -38.81 REMARK 500 PHE A 103 20.24 -142.20 REMARK 500 PRO A 208 149.15 -37.13 REMARK 500 LEU A 215 -12.37 -7.68 REMARK 500 ALA A 225 -167.96 -117.26 REMARK 500 GLN A 227 74.65 89.20 REMARK 500 ASP A 228 4.77 -56.19 REMARK 500 ILE A 229 -168.10 62.46 REMARK 500 ALA A 251 -35.90 67.32 REMARK 500 SER A 276 -112.65 -71.75 REMARK 500 THR A 284 -167.93 177.88 REMARK 500 ILE A 306 -86.18 -99.93 REMARK 500 ALA B 92 172.06 177.77 REMARK 500 PHE B 103 23.83 -147.96 REMARK 500 LEU B 215 32.60 -39.28 REMARK 500 ALA B 225 -162.97 -124.73 REMARK 500 GLN B 227 74.33 73.13 REMARK 500 ASP B 228 -84.42 -41.96 REMARK 500 ILE B 229 -174.48 176.92 REMARK 500 ALA B 251 -36.49 68.16 REMARK 500 SER B 276 -96.14 -67.70 REMARK 500 THR B 284 -170.47 -177.92 REMARK 500 PRO B 295 125.87 -32.67 REMARK 500 ARG X 128 -78.09 -61.39 REMARK 500 VAL Y 2 74.03 -117.33 REMARK 500 TYR Y 3 154.12 -48.71 REMARK 500 ARG Y 14 -99.45 78.76 REMARK 500 LEU Y 15 -17.39 -31.28 REMARK 500 ASN Y 37 43.42 70.86 REMARK 500 ASN Y 46 -152.94 -85.71 REMARK 500 SER Y 50 -91.16 -19.06 REMARK 500 GLN Y 57 58.39 33.94 REMARK 500 ARG Y 68 -5.87 -144.13 REMARK 500 ASN Y 74 71.70 -169.82 REMARK 500 ALA Y 90 -71.08 -56.50 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 SER A 207 PRO A 208 -56.73 REMARK 500 SER A 294 PRO A 295 58.74 REMARK 500 SER B 207 PRO B 208 51.78 REMARK 500 SER B 294 PRO B 295 -54.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 207 -20.86 REMARK 500 SER A 294 33.92 REMARK 500 SER B 207 24.86 REMARK 500 SER B 294 -29.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LZ2 RELATED DB: PDB REMARK 900 RELATED ID: 2LZ2 RELATED DB: PDB REMARK 900 RELATED ID: 3LZ2 RELATED DB: PDB REMARK 900 RELATED ID: 1LZ3 RELATED DB: PDB REMARK 900 RELATED ID: 1LZY RELATED DB: PDB REMARK 900 RELATED ID: 1JEF RELATED DB: PDB REMARK 900 RELATED ID: 1TEW RELATED DB: PDB REMARK 900 RELATED ID: 1JSE RELATED DB: PDB DBREF 1DZB A 1 116 TREMBL CAA05093 CAA05093 1 116 DBREF 1DZB A 117 131 PDB 1DZB 1DZB 117 131 DBREF 1DZB A 201 307 TREMBL CAA05094 CAA05094 1 107 DBREF 1DZB A 308 322 PDB 1DZB 1DZB 308 322 DBREF 1DZB X 1 129 UNP P00703 LYC_MELGA 19 147 DBREF 1DZB B 1 116 TREMBL CAA05093 CAA05093 1 116 DBREF 1DZB B 117 131 PDB 1DZB 1DZB 117 131 DBREF 1DZB B 201 307 TREMBL CAA05094 CAA05094 1 107 DBREF 1DZB B 308 322 PDB 1DZB 1DZB 308 322 DBREF 1DZB Y 1 129 UNP P00703 LYC_MELGA 19 147 SEQRES 1 A 253 GLN VAL LYS LEU GLN GLN SER GLY ALA GLU LEU VAL LYS SEQRES 2 A 253 PRO GLY ALA SER VAL LYS LEU SER CYS THR ALA SER GLY SEQRES 3 A 253 PHE ASN ILE LYS ASP THR TYR MET HIS TRP VAL LYS GLN SEQRES 4 A 253 ARG PRO GLU GLN GLY LEU GLU TRP ILE GLY ARG ILE ASP SEQRES 5 A 253 PRO ALA ASN GLY ASN THR LYS TYR ASP PRO LYS PHE GLN SEQRES 6 A 253 GLY LYS ALA THR ILE THR ALA ASP THR SER SER ASN THR SEQRES 7 A 253 ALA TYR LEU GLN LEU SER SER LEU THR SER GLU ASP THR SEQRES 8 A 253 ALA VAL TYR TYR CYS ALA ARG TRP ASP TRP TYR PHE ASP SEQRES 9 A 253 VAL TRP GLY GLN GLY THR THR VAL THR VAL SER SER GLY SEQRES 10 A 253 GLY GLY GLY SER GLY GLY GLY GLY SER GLY GLY GLY GLY SEQRES 11 A 253 SER ASP ILE GLU LEU THR GLN SER PRO SER SER MET TYR SEQRES 12 A 253 THR SER LEU GLY GLU ARG VAL THR ILE THR CYS LYS ALA SEQRES 13 A 253 SER GLN ASP ILE ASN SER TYR LEU ARG TRP PHE GLN GLN SEQRES 14 A 253 LYS PRO GLY LYS SER PRO LYS THR LEU ILE TYR TYR ALA SEQRES 15 A 253 THR SER LEU ALA ASP GLY VAL PRO SER ARG PHE SER GLY SEQRES 16 A 253 SER GLY SER GLY GLN ASP TYR SER LEU THR ILE SER SER SEQRES 17 A 253 LEU GLU SER ASP ASP THR THR THR TYR TYR CYS LEU GLN SEQRES 18 A 253 HIS GLY GLU SER PRO TYR THR PHE GLY GLY GLY THR LYS SEQRES 19 A 253 LEU GLU ILE LYS ARG ALA ALA ALA GLU GLN LYS LEU ILE SEQRES 20 A 253 SER GLU GLU ASP LEU ASN SEQRES 1 B 253 GLN VAL LYS LEU GLN GLN SER GLY ALA GLU LEU VAL LYS SEQRES 2 B 253 PRO GLY ALA SER VAL LYS LEU SER CYS THR ALA SER GLY SEQRES 3 B 253 PHE ASN ILE LYS ASP THR TYR MET HIS TRP VAL LYS GLN SEQRES 4 B 253 ARG PRO GLU GLN GLY LEU GLU TRP ILE GLY ARG ILE ASP SEQRES 5 B 253 PRO ALA ASN GLY ASN THR LYS TYR ASP PRO LYS PHE GLN SEQRES 6 B 253 GLY LYS ALA THR ILE THR ALA ASP THR SER SER ASN THR SEQRES 7 B 253 ALA TYR LEU GLN LEU SER SER LEU THR SER GLU ASP THR SEQRES 8 B 253 ALA VAL TYR TYR CYS ALA ARG TRP ASP TRP TYR PHE ASP SEQRES 9 B 253 VAL TRP GLY GLN GLY THR THR VAL THR VAL SER SER GLY SEQRES 10 B 253 GLY GLY GLY SER GLY GLY GLY GLY SER GLY GLY GLY GLY SEQRES 11 B 253 SER ASP ILE GLU LEU THR GLN SER PRO SER SER MET TYR SEQRES 12 B 253 THR SER LEU GLY GLU ARG VAL THR ILE THR CYS LYS ALA SEQRES 13 B 253 SER GLN ASP ILE ASN SER TYR LEU ARG TRP PHE GLN GLN SEQRES 14 B 253 LYS PRO GLY LYS SER PRO LYS THR LEU ILE TYR TYR ALA SEQRES 15 B 253 THR SER LEU ALA ASP GLY VAL PRO SER ARG PHE SER GLY SEQRES 16 B 253 SER GLY SER GLY GLN ASP TYR SER LEU THR ILE SER SER SEQRES 17 B 253 LEU GLU SER ASP ASP THR THR THR TYR TYR CYS LEU GLN SEQRES 18 B 253 HIS GLY GLU SER PRO TYR THR PHE GLY GLY GLY THR LYS SEQRES 19 B 253 LEU GLU ILE LYS ARG ALA ALA ALA GLU GLN LYS LEU ILE SEQRES 20 B 253 SER GLU GLU ASP LEU ASN SEQRES 1 X 129 LYS VAL TYR GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 X 129 ARG LEU GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 X 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 X 129 THR HIS ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 X 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 X 129 ASP GLY ARG THR PRO GLY SER LYS ASN LEU CYS ASN ILE SEQRES 7 X 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 X 129 VAL ASN CYS ALA LYS LYS ILE ALA SER GLY GLY ASN GLY SEQRES 9 X 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 X 129 THR ASP VAL HIS ALA TRP ILE ARG GLY CYS ARG LEU SEQRES 1 Y 129 LYS VAL TYR GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 Y 129 ARG LEU GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 Y 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 Y 129 THR HIS ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 Y 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 Y 129 ASP GLY ARG THR PRO GLY SER LYS ASN LEU CYS ASN ILE SEQRES 7 Y 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 Y 129 VAL ASN CYS ALA LYS LYS ILE ALA SER GLY GLY ASN GLY SEQRES 9 Y 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 Y 129 THR ASP VAL HIS ALA TRP ILE ARG GLY CYS ARG LEU FORMUL 5 HOH *260(H2 O) HELIX 1 1 ASN A 28 THR A 32 5 5 HELIX 2 2 PRO A 62 GLN A 65 5 4 HELIX 3 3 THR A 87 THR A 91 5 5 HELIX 4 4 GLU A 279 THR A 283 5 5 HELIX 5 11 ASN B 28 THR B 32 5 5 HELIX 6 12 THR B 87 THR B 91 5 5 HELIX 7 13 GLU B 279 THR B 283 5 5 HELIX 8 5 GLY X 4 LEU X 15 1 12 HELIX 9 6 SER X 24 ASN X 37 1 14 HELIX 10 7 CYS X 80 LEU X 84 5 5 HELIX 11 8 ILE X 88 SER X 100 1 13 HELIX 12 9 TRP X 108 CYS X 115 1 8 HELIX 13 10 ASP X 119 ARG X 125 5 7 HELIX 14 14 GLY Y 4 LYS Y 13 1 10 HELIX 15 15 SER Y 24 ASN Y 37 1 14 HELIX 16 16 CYS Y 80 LEU Y 83 5 4 HELIX 17 17 ILE Y 88 ALA Y 99 1 12 HELIX 18 18 TRP Y 108 CYS Y 115 1 8 HELIX 19 19 ASP Y 119 ILE Y 124 5 6 SHEET 1 A 4 LYS A 3 SER A 7 0 SHEET 2 A 4 VAL A 18 SER A 25 -1 N SER A 25 O LYS A 3 SHEET 3 A 4 THR A 78 LEU A 83 -1 N LEU A 83 O VAL A 18 SHEET 4 A 4 ALA A 68 ASP A 73 -1 N ASP A 73 O THR A 78 SHEET 1 B 6 GLU A 10 VAL A 12 0 SHEET 2 B 6 THR A 110 VAL A 114 1 N THR A 113 O GLU A 10 SHEET 3 B 6 ALA A 92 ALA A 97 -1 N TYR A 94 O THR A 110 SHEET 4 B 6 TYR A 33 ARG A 40 -1 N GLN A 39 O VAL A 93 SHEET 5 B 6 LEU A 45 ASP A 52 -1 N ILE A 51 O MET A 34 SHEET 6 B 6 THR A 58 TYR A 60 -1 N LYS A 59 O ARG A 50 SHEET 1 C 4 THR A 205 SER A 207 0 SHEET 2 C 4 ARG A 218 LYS A 224 -1 N LYS A 224 O THR A 205 SHEET 3 C 4 ASP A 270 SER A 277 -1 N SER A 276 O VAL A 219 SHEET 4 C 4 PHE A 262 SER A 267 -1 N SER A 267 O ASP A 270 SHEET 1 D 5 SER A 210 TYR A 212 0 SHEET 2 D 5 THR A 302 GLU A 305 1 N LYS A 303 O MET A 211 SHEET 3 D 5 THR A 284 GLN A 290 -1 N TYR A 286 O THR A 302 SHEET 4 D 5 LEU A 233 GLN A 238 -1 N GLN A 238 O THR A 285 SHEET 5 D 5 LYS A 245 ILE A 248 -1 N ILE A 248 O TRP A 235 SHEET 1 E 2 THR X 43 ARG X 45 0 SHEET 2 E 2 THR X 51 TYR X 53 -1 N ASP X 52 O ASN X 44 SHEET 1 F 4 LYS B 3 GLN B 6 0 SHEET 2 F 4 VAL B 18 SER B 25 -1 N SER B 25 O LYS B 3 SHEET 3 F 4 THR B 78 LEU B 83 -1 N LEU B 83 O VAL B 18 SHEET 4 F 4 ALA B 68 ASP B 73 -1 N ASP B 73 O THR B 78 SHEET 1 G 6 GLU B 10 VAL B 12 0 SHEET 2 G 6 THR B 110 VAL B 114 1 N THR B 113 O GLU B 10 SHEET 3 G 6 ALA B 92 ALA B 97 -1 N TYR B 94 O THR B 110 SHEET 4 G 6 MET B 34 GLN B 39 -1 N GLN B 39 O VAL B 93 SHEET 5 G 6 LEU B 45 ASP B 52 -1 N ILE B 51 O MET B 34 SHEET 6 G 6 ASN B 57 TYR B 60 -1 N LYS B 59 O ARG B 50 SHEET 1 H 4 THR B 205 SER B 207 0 SHEET 2 H 4 VAL B 219 LYS B 224 -1 N LYS B 224 O THR B 205 SHEET 3 H 4 ASP B 270 ILE B 275 -1 N ILE B 275 O VAL B 219 SHEET 4 H 4 PHE B 262 SER B 267 -1 N SER B 267 O ASP B 270 SHEET 1 I 5 SER B 210 TYR B 212 0 SHEET 2 I 5 THR B 302 GLU B 305 1 N LYS B 303 O MET B 211 SHEET 3 I 5 THR B 284 GLN B 290 -1 N TYR B 286 O THR B 302 SHEET 4 I 5 LEU B 233 GLN B 238 -1 N GLN B 238 O THR B 285 SHEET 5 I 5 LYS B 245 ILE B 248 -1 N ILE B 248 O TRP B 235 SSBOND 1 CYS A 22 CYS A 96 1555 1555 1.98 SSBOND 2 CYS A 223 CYS A 288 1555 1555 2.11 SSBOND 3 CYS B 22 CYS B 96 1555 1555 2.10 SSBOND 4 CYS B 223 CYS B 288 1555 1555 2.09 SSBOND 5 CYS X 6 CYS X 127 1555 1555 2.02 SSBOND 6 CYS X 30 CYS X 115 1555 1555 2.13 SSBOND 7 CYS X 64 CYS X 80 1555 1555 1.99 SSBOND 8 CYS X 76 CYS X 94 1555 1555 2.03 SSBOND 9 CYS Y 6 CYS Y 127 1555 1555 2.04 SSBOND 10 CYS Y 30 CYS Y 115 1555 1555 2.05 SSBOND 11 CYS Y 64 CYS Y 80 1555 1555 2.01 SSBOND 12 CYS Y 76 CYS Y 94 1555 1555 2.02 CRYST1 38.710 112.440 80.000 90.00 97.67 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 0.025833 0.000000 0.003479 0.00000 SCALE2 0.000000 0.008894 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012613 0.00000