PDB Short entry for 1XDT HEADER COMPLEX (TOXIN/GROWTH FACTOR) 18-NOV-97 1XDT TITLE COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH TITLE 2 FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPHTHERIA TOXIN; COMPND 3 CHAIN: T; COMPND 4 SYNONYM: DT; COMPND 5 EC: 2.4.2.36; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HEPARIN-BINDING EPIDERMAL GROWTH FACTOR; COMPND 9 CHAIN: R; COMPND 10 FRAGMENT: EXTRACELLULAR DOMAIN; COMPND 11 SYNONYM: HBEGF; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM DIPHTHERIAE; SOURCE 3 ORGANISM_TAXID: 1717; SOURCE 4 VARIANT: LYSOGENIZED BY THE CORYNEPHAGE BETA; SOURCE 5 CELLULAR_LOCATION: EXTRACELLULAR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 CELLULAR_LOCATION: MEMBRANE-ANCHORED OR EXTRACELLULARLY-RELEASED; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 18 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS COMPLEX (TOXIN-GROWTH FACTOR), DIPHTHERIA TOXIN, RECEPTOR, HEPARIN- KEYWDS 2 BINDING EPIDERMAL GROWTH FACTOR, EPIDERMAL GROWTH FACTOR, COMPLEX KEYWDS 3 (TOXIN-GROWTH FACTOR) COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.V.LOUIE,W.YANG,M.E.BOWMAN,S.CHOE REVDAT 5 09-AUG-23 1XDT 1 REMARK REVDAT 4 13-JUL-11 1XDT 1 VERSN REVDAT 3 24-FEB-09 1XDT 1 VERSN REVDAT 2 01-APR-03 1XDT 1 JRNL REVDAT 1 25-FEB-98 1XDT 0 JRNL AUTH G.V.LOUIE,W.YANG,M.E.BOWMAN,S.CHOE JRNL TITL CRYSTAL STRUCTURE OF THE COMPLEX OF DIPHTHERIA TOXIN WITH AN JRNL TITL 2 EXTRACELLULAR FRAGMENT OF ITS RECEPTOR. JRNL REF MOL.CELL V. 1 67 1997 JRNL REFN ISSN 1097-2765 JRNL PMID 9659904 JRNL DOI 10.1016/S1097-2765(00)80008-8 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.5 REMARK 3 NUMBER OF REFLECTIONS : 15511 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 SET) : 0.172 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 750 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1627 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 90 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 : 4306 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.90 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.340 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.450 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.210 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.230 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.350 ; 2.500 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XDT 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_1000177250. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54532 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 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 (%) : 88.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : 0.05200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.15200 REMARK 200 R SYM FOR SHELL (I) : 0.15200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1MDT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN (15 MG/ML) IN 10 MM TRIS-HCL REMARK 280 (PH 7.5), 0.15 M NACL MIXED WITH AN EQUAL VOLUME OF PRECIPITANT REMARK 280 CONTAINING 50 MM TRIS-HCL (PH 7.5), 0.15 M NACL, 5% (V/V) REMARK 280 GLYCEROL, 22-30% (W/V) POLYETHYLENE GLYCOL 3350; AND REMARK 280 EQUILIBRATED BY VAPOR DIFFUSION AGAINST PRECIPITANT, VAPOR REMARK 280 DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 63.85000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.85000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 44.70000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.85000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.70000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.85000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.85000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 44.70000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.85000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.85000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 44.70000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.85000 REMARK 290 SMTRY3 8 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 300 REMARK: DIPHTHERIA TOXIN MOLECULE HAS THE OPEN CONFORMATION, AND REMARK 300 DIMERIZES WITH ANOTHER DIPHTHERIA TOXIN MOLECULE. 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 12640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, R 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 103.70000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 127.70000 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 LYS T 39 REMARK 465 SER T 40 REMARK 465 GLY T 41 REMARK 465 THR T 42 REMARK 465 GLN T 43 REMARK 465 GLY T 44 REMARK 465 ASN T 189 REMARK 465 ARG T 190 REMARK 465 VAL T 191 REMARK 465 ARG T 192 REMARK 465 ARG T 193 REMARK 465 SER T 194 REMARK 465 VAL T 195 REMARK 465 GLY T 196 REMARK 465 SER T 197 REMARK 465 SER T 198 REMARK 465 LEU T 199 REMARK 465 GLY R 69 REMARK 465 SER R 70 REMARK 465 HIS R 71 REMARK 465 MET R 72 REMARK 465 ARG R 73 REMARK 465 VAL R 74 REMARK 465 THR R 75 REMARK 465 LEU R 76 REMARK 465 SER R 77 REMARK 465 SER R 78 REMARK 465 LYS R 79 REMARK 465 PRO R 80 REMARK 465 GLN R 81 REMARK 465 ALA R 82 REMARK 465 LEU R 83 REMARK 465 ALA R 84 REMARK 465 THR R 85 REMARK 465 PRO R 86 REMARK 465 ASN R 87 REMARK 465 LYS R 88 REMARK 465 GLU R 89 REMARK 465 GLU R 90 REMARK 465 HIS R 91 REMARK 465 GLY R 92 REMARK 465 LYS R 93 REMARK 465 ARG R 94 REMARK 465 LYS R 95 REMARK 465 LYS R 96 REMARK 465 LYS R 97 REMARK 465 GLY R 98 REMARK 465 LYS R 99 REMARK 465 GLY R 100 REMARK 465 LEU R 101 REMARK 465 GLY R 102 REMARK 465 LYS R 103 REMARK 465 LYS R 104 REMARK 465 ARG R 105 REMARK 465 ASP R 106 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 GLU T 70 CD OE1 OE2 REMARK 470 LYS R 113 CG CD CE NZ REMARK 470 ARG R 128 NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ALA T 379 O 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 ARG R 128 NE ARG R 128 CZ 0.169 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 R 128 CD - NE - CZ ANGL. DEV. = -12.7 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 CYS T 201 93.66 -160.77 REMARK 500 ASN T 235 -3.21 53.42 REMARK 500 THR T 269 -62.16 -91.57 REMARK 500 ALA T 317 148.81 -175.01 REMARK 500 VAL T 347 0.19 -163.14 REMARK 500 GLU T 349 54.98 -172.35 REMARK 500 LEU T 350 -158.89 -152.70 REMARK 500 ASP T 352 -44.59 12.07 REMARK 500 ILE T 353 -39.02 -133.50 REMARK 500 TYR T 358 -95.73 -95.79 REMARK 500 LYS T 385 -128.96 41.93 REMARK 500 ASP T 392 25.39 45.81 REMARK 500 ASN T 424 -93.77 -152.43 REMARK 500 HIS T 520 -4.04 75.83 REMARK 500 ARG R 110 -96.05 -77.57 REMARK 500 TYR R 112 39.47 -89.82 REMARK 500 ASP R 114 -1.14 67.04 REMARK 500 ILE R 117 -82.78 -85.55 REMARK 500 HIS R 118 48.82 -95.85 REMARK 500 REMARK 500 REMARK: NULL DBREF 1XDT T 1 535 UNP P00588 DTX_CORBE 33 567 DBREF 1XDT R 73 147 UNP Q99075 HBEGF_HUMAN 73 147 SEQRES 1 T 535 GLY ALA ASP ASP VAL VAL ASP SER SER LYS SER PHE VAL SEQRES 2 T 535 MET GLU ASN PHE SER SER TYR HIS GLY THR LYS PRO GLY SEQRES 3 T 535 TYR VAL ASP SER ILE GLN LYS GLY ILE GLN LYS PRO LYS SEQRES 4 T 535 SER GLY THR GLN GLY ASN TYR ASP ASP ASP TRP LYS GLY SEQRES 5 T 535 PHE TYR SER THR ASP ASN LYS TYR ASP ALA ALA GLY TYR SEQRES 6 T 535 SER VAL ASP ASN GLU ASN PRO LEU SER GLY LYS ALA GLY SEQRES 7 T 535 GLY VAL VAL LYS VAL THR TYR PRO GLY LEU THR LYS VAL SEQRES 8 T 535 LEU ALA LEU LYS VAL ASP ASN ALA GLU THR ILE LYS LYS SEQRES 9 T 535 GLU LEU GLY LEU SER LEU THR GLU PRO LEU MET GLU GLN SEQRES 10 T 535 VAL GLY THR GLU GLU PHE ILE LYS ARG PHE GLY ASP GLY SEQRES 11 T 535 ALA SER ARG VAL VAL LEU SER LEU PRO PHE ALA GLU GLY SEQRES 12 T 535 SER SER SER VAL GLU TYR ILE ASN ASN TRP GLU GLN ALA SEQRES 13 T 535 LYS ALA LEU SER VAL GLU LEU GLU ILE ASN PHE GLU THR SEQRES 14 T 535 ARG GLY LYS ARG GLY GLN ASP ALA MET TYR GLU TYR MET SEQRES 15 T 535 ALA GLN ALA CYS ALA GLY ASN ARG VAL ARG ARG SER VAL SEQRES 16 T 535 GLY SER SER LEU SER CYS ILE ASN LEU ASP TRP ASP VAL SEQRES 17 T 535 ILE ARG ASP LYS THR LYS THR LYS ILE GLU SER LEU LYS SEQRES 18 T 535 GLU HIS GLY PRO ILE LYS ASN LYS MET SER GLU SER PRO SEQRES 19 T 535 ASN LYS THR VAL SER GLU GLU LYS ALA LYS GLN TYR LEU SEQRES 20 T 535 GLU GLU PHE HIS GLN THR ALA LEU GLU HIS PRO GLU LEU SEQRES 21 T 535 SER GLU LEU LYS THR VAL THR GLY THR ASN PRO VAL PHE SEQRES 22 T 535 ALA GLY ALA ASN TYR ALA ALA TRP ALA VAL ASN VAL ALA SEQRES 23 T 535 GLN VAL ILE ASP SER GLU THR ALA ASP ASN LEU GLU LYS SEQRES 24 T 535 THR THR ALA ALA LEU SER ILE LEU PRO GLY ILE GLY SER SEQRES 25 T 535 VAL MET GLY ILE ALA ASP GLY ALA VAL HIS HIS ASN THR SEQRES 26 T 535 GLU GLU ILE VAL ALA GLN SER ILE ALA LEU SER SER LEU SEQRES 27 T 535 MET VAL ALA GLN ALA ILE PRO LEU VAL GLY GLU LEU VAL SEQRES 28 T 535 ASP ILE GLY PHE ALA ALA TYR ASN PHE VAL GLU SER ILE SEQRES 29 T 535 ILE ASN LEU PHE GLN VAL VAL HIS ASN SER TYR ASN ARG SEQRES 30 T 535 PRO ALA TYR SER PRO GLY HIS LYS THR GLN PRO PHE LEU SEQRES 31 T 535 HIS ASP GLY TYR ALA VAL SER TRP ASN THR VAL GLU ASP SEQRES 32 T 535 SER ILE ILE ARG THR GLY PHE GLN GLY GLU SER GLY HIS SEQRES 33 T 535 ASP ILE LYS ILE THR ALA GLU ASN THR PRO LEU PRO ILE SEQRES 34 T 535 ALA GLY VAL LEU LEU PRO THR ILE PRO GLY LYS LEU ASP SEQRES 35 T 535 VAL ASN LYS SER LYS THR HIS ILE SER VAL ASN GLY ARG SEQRES 36 T 535 LYS ILE ARG MET ARG CYS ARG ALA ILE ASP GLY ASP VAL SEQRES 37 T 535 THR PHE CYS ARG PRO LYS SER PRO VAL TYR VAL GLY ASN SEQRES 38 T 535 GLY VAL HIS ALA ASN LEU HIS VAL ALA PHE HIS ARG SER SEQRES 39 T 535 SER SER GLU LYS ILE HIS SER ASN GLU ILE SER SER ASP SEQRES 40 T 535 SER ILE GLY VAL LEU GLY TYR GLN LYS THR VAL ASP HIS SEQRES 41 T 535 THR LYS VAL ASN SER LYS LEU SER LEU PHE PHE GLU ILE SEQRES 42 T 535 LYS SER SEQRES 1 R 79 GLY SER HIS MET ARG VAL THR LEU SER SER LYS PRO GLN SEQRES 2 R 79 ALA LEU ALA THR PRO ASN LYS GLU GLU HIS GLY LYS ARG SEQRES 3 R 79 LYS LYS LYS GLY LYS GLY LEU GLY LYS LYS ARG ASP PRO SEQRES 4 R 79 CYS LEU ARG LYS TYR LYS ASP PHE CYS ILE HIS GLY GLU SEQRES 5 R 79 CYS LYS TYR VAL LYS GLU LEU ARG ALA PRO SER CYS ILE SEQRES 6 R 79 CYS HIS PRO GLY TYR HIS GLY GLU ARG CYS HIS GLY LEU SEQRES 7 R 79 SER FORMUL 3 HOH *48(H2 O) HELIX 1 3 VAL T 28 LYS T 33 1 6 HELIX 2 5 LYS T 59 SER T 66 1 8 HELIX 3 6 ALA T 99 GLU T 105 1 7 HELIX 4 7 LEU T 114 GLN T 117 1 4 HELIX 5 8 GLU T 121 ARG T 126 1 6 HELIX 6 9 GLN T 155 ALA T 158 5 4 HELIX 7 11 ASP T 176 ALA T 185 1 10 HELIX 8 12 TRP T 206 LYS T 221 1 16 HELIX 9 13 GLY T 224 GLU T 232 1 9 HELIX 10 14 GLU T 240 GLU T 256 1 17 HELIX 11 15 PRO T 258 THR T 267 5 10 HELIX 12 17 GLY T 275 VAL T 288 1 14 HELIX 13 18 SER T 291 ASP T 295 1 5 HELIX 14 19 LEU T 297 ILE T 306 1 10 HELIX 15 20 ILE T 310 MET T 314 1 5 HELIX 16 21 GLU T 326 VAL T 347 1 22 HELIX 17 22 GLY T 354 ALA T 357 1 4 HELIX 18 23 ASN T 359 ASN T 376 1 18 HELIX 19 24 VAL T 401 SER T 404 5 4 HELIX 20 26 LYS R 125 LEU R 127 5 3 SHEET 1 A 5 PHE T 12 GLU T 15 0 SHEET 2 A 5 LEU T 88 ALA T 93 -1 N VAL T 91 O PHE T 12 SHEET 3 A 5 ARG T 133 PRO T 139 1 N ARG T 133 O LYS T 90 SHEET 4 A 5 VAL T 147 ASN T 151 -1 N ILE T 150 O LEU T 136 SHEET 5 A 5 PHE T 53 THR T 56 -1 N SER T 55 O TYR T 149 SHEET 1 B 3 SER T 18 THR T 23 0 SHEET 2 B 3 GLY T 79 TYR T 85 -1 N VAL T 83 O SER T 19 SHEET 3 B 3 LEU T 159 ASN T 166 -1 N ILE T 165 O VAL T 80 SHEET 1 C 6 PHE T 389 HIS T 391 0 SHEET 2 C 6 TYR T 394 TRP T 398 -1 N VAL T 396 O PHE T 389 SHEET 3 C 6 GLY T 412 ALA T 422 -1 N THR T 421 O ALA T 395 SHEET 4 C 6 ALA T 485 ARG T 493 -1 N ARG T 493 O GLY T 412 SHEET 5 C 6 HIS T 449 VAL T 452 -1 N SER T 451 O ASN T 486 SHEET 6 C 6 ARG T 455 ARG T 458 -1 N ILE T 457 O ILE T 450 SHEET 1 D 2 ILE T 405 ARG T 407 0 SHEET 2 D 2 GLU T 532 LYS T 534 1 N GLU T 532 O ILE T 406 SHEET 1 E 5 MET T 459 ALA T 463 0 SHEET 2 E 5 VAL T 468 PRO T 473 -1 N ARG T 472 O ARG T 460 SHEET 3 E 5 GLY T 431 PRO T 435 -1 N LEU T 434 O THR T 469 SHEET 4 E 5 SER T 508 LEU T 512 -1 N LEU T 512 O GLY T 431 SHEET 5 E 5 LYS T 526 PHE T 530 -1 N LEU T 529 O ILE T 509 SHEET 1 F 2 GLN T 515 VAL T 518 0 SHEET 2 F 2 THR T 521 ASN T 524 -1 N VAL T 523 O LYS T 516 SHEET 1 G 2 GLY R 119 CYS R 121 0 SHEET 2 G 2 CYS R 132 CYS R 134 -1 N ILE R 133 O GLU R 120 SSBOND 1 CYS T 186 CYS T 201 1555 1555 2.04 SSBOND 2 CYS T 461 CYS T 471 1555 1555 2.04 SSBOND 3 CYS R 108 CYS R 121 1555 1555 2.03 SSBOND 4 CYS R 116 CYS R 132 1555 1555 2.04 SSBOND 5 CYS R 134 CYS R 143 1555 1555 2.03 CRYST1 89.400 103.700 127.700 90.00 90.00 90.00 C 2 2 21 8 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 0.011186 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007831 0.00000