PDB Short entry for 1NOY HEADER TRANSFERASE/DNA 16-FEB-96 1NOY TITLE DNA POLYMERASE (E.C.2.7.7.7)/DNA COMPLEX CAVEAT 1NOY INCORRECT CHIRAL CENTER(S) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*TP*T)-3'); COMPND 3 CHAIN: S; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROTEIN (DNA POLYMERASE (E.C.2.7.7.7)); COMPND 7 CHAIN: A, B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 5 ORGANISM_TAXID: 10665; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EXONUCLEASE, DNA-BINDING, COMPLEX KEYWDS 2 (NUCLEOTIDYLTRANSFERASE/DNA) EXPDTA X-RAY DIFFRACTION AUTHOR J.WANG,P.YU,T.C.LIN,W.H.KONIGSBERG,T.A.STEITZ REVDAT 2 24-FEB-09 1NOY 1 VERSN REVDAT 1 14-OCT-96 1NOY 0 JRNL AUTH J.WANG,P.YU,T.C.LIN,W.H.KONIGSBERG,T.A.STEITZ JRNL TITL CRYSTAL STRUCTURES OF AN NH2-TERMINAL FRAGMENT OF JRNL TITL 2 T4 DNA POLYMERASE AND ITS COMPLEXES WITH JRNL TITL 3 SINGLE-STRANDED DNA AND WITH DIVALENT METAL IONS. JRNL REF BIOCHEMISTRY V. 35 8110 1996 JRNL REFN ISSN 0006-2960 JRNL PMID 8679562 JRNL DOI 10.1021/BI960178R REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.C.LIN,G.KARAM,W.H.KONIGSBERG REMARK 1 TITL ISOLATION, CHARACTERIZATION, AND KINETIC REMARK 1 TITL 2 PROPERTIES OF TRUNCATED FORMS OF T4 DNA POLYMERASE REMARK 1 TITL 3 THAT EXHIBIT 3'-5' EXONUCLEASE ACTIVITY REMARK 1 REF J.BIOL.CHEM. V. 269 19286 1994 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.K.SPICER,J.RUSH,C.FUNG,L.J.REHA-KRANTZ,J.D.KARAM, REMARK 1 AUTH 2 W.H.KONIGSBERG REMARK 1 TITL PRIMARY STRUCTURE OF T4 DNA POLYMERASE. REMARK 1 TITL 2 EVOLUTIONARY RELATEDNESS TO EUCARYOTIC AND OTHER REMARK 1 TITL 3 PROCARYOTIC DNA POLYMERASES REMARK 1 REF J.BIOL.CHEM. V. 263 7478 1988 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 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 : 37292 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) : 0.222 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 : 5892 REMARK 3 NUCLEIC ACID ATOMS : 57 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 179 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.54 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: THIS STRUCTURE WAS DETERMINED AT REMARK 3 ROOM TEMPERATURE (298K). THE DIVALENT AND P(DT)3 WERE REMARK 3 DETERMINED FROM TWO SEPARATE EXPERIMENTS AT LOWER RESOLUTIONS, REMARK 3 CONCATENATED TOGETHER IN THIS ENTRY. ASP 1, GLU 2, ILE 211 AND REMARK 3 FOUR OTHER RESIDUES WERE IDENTIFIED FROM ELECTRON DENSITY REMARK 3 MAPS, BUT THE AUTHORS HAVE NOT DONE DNA SEQUENCING TO CONFIRM REMARK 3 POSSIBLE SPONTANEOUSLY MUTATIONS. ILE 211 WAS REPLACED BY THR REMARK 3 211 IN THIS ENTRY WITHOUT ADDITIONAL REFINEMENT BY REMOVING REMARK 3 ATOM CD1. REMARK 4 REMARK 4 1NOY 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 : 07-OCT-93 REMARK 200 TEMPERATURE (KELVIN) : 298.00 REMARK 200 PH : NULL 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) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SDMS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DCREDUCE REMARK 200 DATA SCALING SOFTWARE : SCALEPACK 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 (%) : 100.0 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 57.35050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.82800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 57.35050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.82800 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: S, 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 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 MET A 1 REMARK 465 HIS A 374 REMARK 465 LYS A 375 REMARK 465 VAL A 376 REMARK 465 ILE A 377 REMARK 465 PRO A 378 REMARK 465 GLN A 379 REMARK 465 GLN A 380 REMARK 465 GLY A 381 REMARK 465 SER A 382 REMARK 465 HIS A 383 REMARK 465 VAL A 384 REMARK 465 LYS A 385 REMARK 465 GLN A 386 REMARK 465 SER A 387 REMARK 465 PHE A 388 REMARK 465 MET B 1 REMARK 465 GLU B 44 REMARK 465 SER B 45 REMARK 465 LYS B 46 REMARK 465 TYR B 47 REMARK 465 LYS B 48 REMARK 465 ASP B 49 REMARK 465 ILE B 50 REMARK 465 TYR B 51 REMARK 465 MET B 73 REMARK 465 GLU B 74 REMARK 465 ASP B 75 REMARK 465 ILE B 76 REMARK 465 GLY B 77 REMARK 465 LEU B 78 REMARK 465 GLU B 79 REMARK 465 ALA B 80 REMARK 465 LEU B 81 REMARK 465 LEU B 250 REMARK 465 GLN B 251 REMARK 465 ASN B 252 REMARK 465 MET B 253 REMARK 465 TYR B 254 REMARK 465 GLY B 255 REMARK 465 LYS B 371 REMARK 465 GLY B 372 REMARK 465 GLU B 373 REMARK 465 HIS B 374 REMARK 465 LYS B 375 REMARK 465 VAL B 376 REMARK 465 ILE B 377 REMARK 465 PRO B 378 REMARK 465 GLN B 379 REMARK 465 GLN B 380 REMARK 465 GLY B 381 REMARK 465 SER B 382 REMARK 465 HIS B 383 REMARK 465 VAL B 384 REMARK 465 LYS B 385 REMARK 465 GLN B 386 REMARK 465 SER B 387 REMARK 465 PHE B 388 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 SER B 256 OG 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 OP1 DT S 4 O HOH S 96 0.87 REMARK 500 MN MN B 3000 O HOH B 3032 1.33 REMARK 500 O4' DT S 3 O HOH S 116 1.67 REMARK 500 O2 DT S 5 NZ LYS B 119 1.84 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 DT S 3 C5 DT S 3 C6 0.051 REMARK 500 DT S 3 C5 DT S 3 C7 0.080 REMARK 500 DT S 4 P DT S 4 OP1 0.124 REMARK 500 DT S 4 C5' DT S 4 C4' 0.097 REMARK 500 DT S 4 C5 DT S 4 C7 0.054 REMARK 500 DT S 5 C3' DT S 5 C2' -0.053 REMARK 500 DT S 5 C5 DT S 5 C7 0.073 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 DT S 3 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT S 3 N3 - C4 - O4 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT S 4 O5' - P - OP1 ANGL. DEV. = -12.8 DEGREES REMARK 500 DT S 4 O5' - P - OP2 ANGL. DEV. = 14.1 DEGREES REMARK 500 DT S 4 P - O5' - C5' ANGL. DEV. = 9.7 DEGREES REMARK 500 DT S 4 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT S 4 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT S 4 O3' - P - O5' ANGL. DEV. = -14.3 DEGREES REMARK 500 DT S 4 O3' - P - OP2 ANGL. DEV. = 27.3 DEGREES REMARK 500 DT S 4 O3' - P - OP1 ANGL. DEV. = -17.4 DEGREES REMARK 500 DT S 5 O4' - C4' - C3' ANGL. DEV. = 5.4 DEGREES REMARK 500 DT S 5 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 DT S 5 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT S 5 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT S 5 O3' - P - O5' ANGL. DEV. = -26.0 DEGREES REMARK 500 DT S 5 O3' - P - OP2 ANGL. DEV. = 23.1 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 GLU A 3 101.86 80.13 REMARK 500 ASP A 21 -155.69 -75.11 REMARK 500 GLU A 44 -59.60 -150.89 REMARK 500 SER A 45 78.20 -50.16 REMARK 500 ASN A 54 -163.22 -160.13 REMARK 500 TYR A 95 69.95 -117.92 REMARK 500 PRO A 121 82.42 -68.91 REMARK 500 ALA A 132 143.28 -170.45 REMARK 500 PHE A 218 -69.64 -122.26 REMARK 500 GLN A 251 -156.38 -175.13 REMARK 500 ASN A 252 -122.04 71.78 REMARK 500 SER A 256 70.54 -69.01 REMARK 500 PHE A 279 50.51 71.38 REMARK 500 ASN A 307 1.48 -67.72 REMARK 500 ASN A 313 70.01 -155.86 REMARK 500 LYS A 349 60.46 61.23 REMARK 500 LYS A 371 50.04 39.27 REMARK 500 GLU B 3 105.11 73.12 REMARK 500 ILE B 6 -33.43 -133.55 REMARK 500 GLU B 22 -56.05 -5.30 REMARK 500 ASN B 23 41.72 -79.55 REMARK 500 ASN B 54 -145.68 -150.32 REMARK 500 LYS B 71 -29.41 80.85 REMARK 500 SER B 97 166.86 82.89 REMARK 500 LYS B 119 139.10 -32.53 REMARK 500 PRO B 121 97.15 -59.77 REMARK 500 ASN B 150 7.21 -176.46 REMARK 500 MET B 152 -61.30 1.00 REMARK 500 TYR B 153 -13.14 -48.84 REMARK 500 ALA B 165 -57.17 -175.56 REMARK 500 LEU B 167 164.81 -42.26 REMARK 500 GLU B 174 64.97 -69.37 REMARK 500 ASP B 219 -70.28 -42.95 REMARK 500 ILE B 230 -86.44 -99.53 REMARK 500 LEU B 231 -5.90 -56.29 REMARK 500 ARG B 234 -31.19 152.94 REMARK 500 ASN B 281 75.89 -101.30 REMARK 500 LYS B 296 -40.78 76.50 REMARK 500 TYR B 302 -157.16 -63.78 REMARK 500 ASP B 303 73.82 -177.98 REMARK 500 PRO B 305 -155.24 -73.53 REMARK 500 ILE B 306 -79.16 -131.64 REMARK 500 LEU B 309 -50.43 -29.74 REMARK 500 THR B 312 34.57 -81.14 REMARK 500 ASN B 313 70.06 134.65 REMARK 500 HIS B 314 -169.82 -70.21 REMARK 500 GLN B 315 -58.68 71.22 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 DT S 5 0.13 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 481 DISTANCE = 5.57 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 B2000 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 114 OE2 REMARK 620 2 ASP B 324 OD2 153.8 REMARK 620 3 DT S 5 OP1 111.4 94.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 2000 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 3000 DBREF 1NOY A 1 388 UNP P04415 DPOL_BPT4 1 388 DBREF 1NOY B 1 388 UNP P04415 DPOL_BPT4 1 388 DBREF 1NOY S 3 5 PDB 1NOY 1NOY 3 5 SEQADV 1NOY ASP A 2 UNP P04415 LYS 2 CONFLICT SEQADV 1NOY LEU A 250 UNP P04415 ILE 250 CONFLICT SEQADV 1NOY ASP B 2 UNP P04415 LYS 2 CONFLICT SEQADV 1NOY LEU B 250 UNP P04415 ILE 250 CONFLICT SEQRES 1 S 3 DT DT DT SEQRES 1 A 388 MET ASP GLU PHE TYR ILE SER ILE GLU THR VAL GLY ASN SEQRES 2 A 388 ASN ILE VAL GLU ARG TYR ILE ASP GLU ASN GLY LYS GLU SEQRES 3 A 388 ARG THR ARG GLU VAL GLU TYR LEU PRO THR MET PHE ARG SEQRES 4 A 388 HIS CYS LYS GLU GLU SER LYS TYR LYS ASP ILE TYR GLY SEQRES 5 A 388 LYS ASN CYS ALA PRO GLN LYS PHE PRO SER MET LYS ASP SEQRES 6 A 388 ALA ARG ASP TRP MET LYS ARG MET GLU ASP ILE GLY LEU SEQRES 7 A 388 GLU ALA LEU GLY MET ASN ASP PHE LYS LEU ALA TYR ILE SEQRES 8 A 388 SER ASP THR TYR GLY SER GLU ILE VAL TYR ASP ARG LYS SEQRES 9 A 388 PHE VAL ARG VAL ALA ASN CYS ASP ILE GLU VAL THR GLY SEQRES 10 A 388 ASP LYS PHE PRO ASP PRO MET LYS ALA GLU TYR GLU ILE SEQRES 11 A 388 ASP ALA ILE THR HIS TYR ASP SER ILE ASP ASP ARG PHE SEQRES 12 A 388 TYR VAL PHE ASP LEU LEU ASN SER MET TYR GLY SER VAL SEQRES 13 A 388 SER LYS TRP ASP ALA LYS LEU ALA ALA LYS LEU ASP CYS SEQRES 14 A 388 GLU GLY GLY ASP GLU VAL PRO GLN GLU ILE LEU ASP ARG SEQRES 15 A 388 VAL ILE TYR MET PRO PHE ASP ASN GLU ARG ASP MET LEU SEQRES 16 A 388 MET GLU TYR ILE ASN LEU TRP GLU GLN LYS ARG PRO ALA SEQRES 17 A 388 ILE PHE THR GLY TRP ASN ILE GLU GLY PHE ASP VAL PRO SEQRES 18 A 388 TYR ILE MET ASN ARG VAL LYS MET ILE LEU GLY GLU ARG SEQRES 19 A 388 SER MET LYS ARG PHE SER PRO ILE GLY ARG VAL LYS SER SEQRES 20 A 388 LYS LEU LEU GLN ASN MET TYR GLY SER LYS GLU ILE TYR SEQRES 21 A 388 SER ILE ASP GLY VAL SER ILE LEU ASP TYR LEU ASP LEU SEQRES 22 A 388 TYR LYS LYS PHE ALA PHE THR ASN LEU PRO SER PHE SER SEQRES 23 A 388 LEU GLU SER VAL ALA GLN HIS GLU THR LYS LYS GLY LYS SEQRES 24 A 388 LEU PRO TYR ASP GLY PRO ILE ASN LYS LEU ARG GLU THR SEQRES 25 A 388 ASN HIS GLN ARG TYR ILE SER TYR ASN ILE ILE ASP VAL SEQRES 26 A 388 GLU SER VAL GLN ALA ILE ASP LYS ILE ARG GLY PHE ILE SEQRES 27 A 388 ASP LEU VAL LEU SER MET SER TYR TYR ALA LYS MET PRO SEQRES 28 A 388 PHE SER GLY VAL MET SER PRO ILE LYS THR TRP ASP ALA SEQRES 29 A 388 ILE ILE PHE ASN SER LEU LYS GLY GLU HIS LYS VAL ILE SEQRES 30 A 388 PRO GLN GLN GLY SER HIS VAL LYS GLN SER PHE SEQRES 1 B 388 MET ASP GLU PHE TYR ILE SER ILE GLU THR VAL GLY ASN SEQRES 2 B 388 ASN ILE VAL GLU ARG TYR ILE ASP GLU ASN GLY LYS GLU SEQRES 3 B 388 ARG THR ARG GLU VAL GLU TYR LEU PRO THR MET PHE ARG SEQRES 4 B 388 HIS CYS LYS GLU GLU SER LYS TYR LYS ASP ILE TYR GLY SEQRES 5 B 388 LYS ASN CYS ALA PRO GLN LYS PHE PRO SER MET LYS ASP SEQRES 6 B 388 ALA ARG ASP TRP MET LYS ARG MET GLU ASP ILE GLY LEU SEQRES 7 B 388 GLU ALA LEU GLY MET ASN ASP PHE LYS LEU ALA TYR ILE SEQRES 8 B 388 SER ASP THR TYR GLY SER GLU ILE VAL TYR ASP ARG LYS SEQRES 9 B 388 PHE VAL ARG VAL ALA ASN CYS ASP ILE GLU VAL THR GLY SEQRES 10 B 388 ASP LYS PHE PRO ASP PRO MET LYS ALA GLU TYR GLU ILE SEQRES 11 B 388 ASP ALA ILE THR HIS TYR ASP SER ILE ASP ASP ARG PHE SEQRES 12 B 388 TYR VAL PHE ASP LEU LEU ASN SER MET TYR GLY SER VAL SEQRES 13 B 388 SER LYS TRP ASP ALA LYS LEU ALA ALA LYS LEU ASP CYS SEQRES 14 B 388 GLU GLY GLY ASP GLU VAL PRO GLN GLU ILE LEU ASP ARG SEQRES 15 B 388 VAL ILE TYR MET PRO PHE ASP ASN GLU ARG ASP MET LEU SEQRES 16 B 388 MET GLU TYR ILE ASN LEU TRP GLU GLN LYS ARG PRO ALA SEQRES 17 B 388 ILE PHE THR GLY TRP ASN ILE GLU GLY PHE ASP VAL PRO SEQRES 18 B 388 TYR ILE MET ASN ARG VAL LYS MET ILE LEU GLY GLU ARG SEQRES 19 B 388 SER MET LYS ARG PHE SER PRO ILE GLY ARG VAL LYS SER SEQRES 20 B 388 LYS LEU LEU GLN ASN MET TYR GLY SER LYS GLU ILE TYR SEQRES 21 B 388 SER ILE ASP GLY VAL SER ILE LEU ASP TYR LEU ASP LEU SEQRES 22 B 388 TYR LYS LYS PHE ALA PHE THR ASN LEU PRO SER PHE SER SEQRES 23 B 388 LEU GLU SER VAL ALA GLN HIS GLU THR LYS LYS GLY LYS SEQRES 24 B 388 LEU PRO TYR ASP GLY PRO ILE ASN LYS LEU ARG GLU THR SEQRES 25 B 388 ASN HIS GLN ARG TYR ILE SER TYR ASN ILE ILE ASP VAL SEQRES 26 B 388 GLU SER VAL GLN ALA ILE ASP LYS ILE ARG GLY PHE ILE SEQRES 27 B 388 ASP LEU VAL LEU SER MET SER TYR TYR ALA LYS MET PRO SEQRES 28 B 388 PHE SER GLY VAL MET SER PRO ILE LYS THR TRP ASP ALA SEQRES 29 B 388 ILE ILE PHE ASN SER LEU LYS GLY GLU HIS LYS VAL ILE SEQRES 30 B 388 PRO GLN GLN GLY SER HIS VAL LYS GLN SER PHE HET ZN B2000 1 HET MN B3000 1 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION FORMUL 4 ZN ZN 2+ FORMUL 5 MN MN 2+ FORMUL 6 HOH *179(H2 O) HELIX 1 1 HIS A 40 GLU A 43 5 4 HELIX 2 2 MET A 63 ILE A 76 1 14 HELIX 3 3 LEU A 81 THR A 94 5 14 HELIX 4 4 ARG A 103 PHE A 105 5 3 HELIX 5 5 ALA A 161 ALA A 165 1 5 HELIX 6 6 ASP A 168 GLU A 170 5 3 HELIX 7 7 GLN A 177 ARG A 182 1 6 HELIX 8 8 GLU A 191 GLN A 204 1 14 HELIX 9 9 ASP A 219 PHE A 239 1 21 HELIX 10 10 ASN A 252 TYR A 254 5 3 HELIX 11 11 TYR A 270 PHE A 277 1 8 HELIX 12 12 LEU A 287 THR A 295 1 9 HELIX 13 13 ILE A 306 ARG A 335 5 30 HELIX 14 14 PHE A 337 ALA A 348 1 12 HELIX 15 15 PHE A 352 MET A 356 5 5 HELIX 16 16 PRO A 358 SER A 369 1 12 HELIX 17 17 HIS B 40 LYS B 42 5 3 HELIX 18 18 MET B 63 ARG B 67 1 5 HELIX 19 19 MET B 83 THR B 94 5 12 HELIX 20 20 ARG B 103 PHE B 105 5 3 HELIX 21 21 GLN B 177 ARG B 182 1 6 HELIX 22 22 GLU B 191 GLN B 204 1 14 HELIX 23 23 ASP B 219 MET B 229 1 11 HELIX 24 24 MET B 236 ARG B 238 5 3 HELIX 25 25 TYR B 270 PHE B 277 1 8 HELIX 26 26 LEU B 287 THR B 295 1 9 HELIX 27 27 ASN B 307 ASN B 313 5 7 HELIX 28 28 ARG B 316 ARG B 335 1 20 HELIX 29 29 PHE B 337 ALA B 348 1 12 HELIX 30 30 PHE B 352 MET B 356 5 5 HELIX 31 31 PRO B 358 ASN B 368 1 11 SHEET 1 A 3 GLU A 26 GLU A 32 0 SHEET 2 A 3 ASN A 14 ILE A 20 -1 N TYR A 19 O ARG A 27 SHEET 3 A 3 PHE A 4 VAL A 11 -1 N VAL A 11 O ASN A 14 SHEET 1 B 5 ILE A 209 THR A 211 0 SHEET 2 B 5 VAL A 108 VAL A 115 1 N ALA A 109 O ILE A 209 SHEET 3 B 5 ILE A 130 ASP A 137 -1 N TYR A 136 O ASN A 110 SHEET 4 B 5 ARG A 142 LEU A 148 -1 N PHE A 146 O ILE A 133 SHEET 5 B 5 VAL A 183 PHE A 188 1 N ILE A 184 O PHE A 143 SHEET 1 C 2 VAL A 245 LEU A 249 0 SHEET 2 C 2 GLU A 258 ILE A 262 -1 N SER A 261 O LYS A 246 SHEET 1 D 3 LYS B 25 VAL B 31 0 SHEET 2 D 3 ASN B 14 ASP B 21 -1 N ASP B 21 O LYS B 25 SHEET 3 D 3 PHE B 4 VAL B 11 -1 N VAL B 11 O ASN B 14 SHEET 1 E 5 ILE B 209 THR B 211 0 SHEET 2 E 5 VAL B 108 GLU B 114 1 N ALA B 109 O ILE B 209 SHEET 3 E 5 ALA B 132 ASP B 137 -1 N TYR B 136 O ASN B 110 SHEET 4 E 5 ARG B 142 LEU B 148 -1 N PHE B 146 O ILE B 133 SHEET 5 E 5 VAL B 183 PHE B 188 1 N ILE B 184 O PHE B 143 SHEET 1 F 2 VAL B 245 LYS B 248 0 SHEET 2 F 2 ILE B 259 ILE B 262 -1 N SER B 261 O LYS B 246 SSBOND 1 CYS A 41 CYS A 55 1555 1555 2.04 SSBOND 2 CYS B 41 CYS B 55 1555 1555 2.01 LINK ZN ZN B2000 OE2 GLU B 114 1555 1555 2.55 LINK ZN ZN B2000 OD2 ASP B 324 1555 1555 2.59 LINK ZN ZN B2000 OP1 DT S 5 1555 1555 2.70 LINK MN MN B3000 O HOH S 108 1555 1555 2.06 SITE 1 AC1 4 ASP B 112 GLU B 114 ASP B 324 DT S 5 SITE 1 AC2 5 ASP B 112 HOH B3032 DT S 4 DT S 5 SITE 2 AC2 5 HOH S 108 CRYST1 114.701 109.656 70.268 90.00 90.00 90.00 P 21 21 2 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 0.008718 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009119 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014231 0.00000