PDB Short entry for 1UBD HEADER TRANSCRIPTION/DNA 04-OCT-96 1UBD TITLE CO-CRYSTAL STRUCTURE OF HUMAN YY1 ZINC FINGER DOMAIN BOUND TO THE TITLE 2 ADENO-ASSOCIATED VIRUS P5 INITIATOR ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*GP*GP*GP*TP*CP*TP*CP*CP*AP*TP*TP*TP*TP*GP*AP*A P*GP*CP*G)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'- COMPND 8 D(*CP*GP*CP*TP*TP*CP*AP*AP*AP*AP*TP*GP*GP*AP*GP*AP*C P*CP*CP*T)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: PROTEIN (YY1 ZINC FINGER DOMAIN); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION INITIATION, INITIATOR ELEMENT, YY1, ZINC FINGER KEYWDS 2 PROTEIN, DNA- PROTEIN RECOGNITION, COMPLEX (TRANSCRIPTION KEYWDS 3 REGULATION-DNA), TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.B.HOUBAVIY,A.USHEVA,T.SHENK,S.K.BURLEY REVDAT 5 14-FEB-24 1UBD 1 REMARK REVDAT 4 03-NOV-21 1UBD 1 SEQADV REVDAT 3 03-FEB-21 1UBD 1 AUTHOR JRNL REMARK LINK REVDAT 2 24-FEB-09 1UBD 1 VERSN REVDAT 1 23-DEC-96 1UBD 0 JRNL AUTH H.B.HOUBAVIY,A.USHEVA,T.SHENK,S.K.BURLEY JRNL TITL COCRYSTAL STRUCTURE OF YY1 BOUND TO THE ADENO-ASSOCIATED JRNL TITL 2 VIRUS P5 INITIATOR. JRNL REF PROC.NATL.ACAD.SCI.USA V. 93 13577 1996 JRNL REFN ISSN 0027-8424 JRNL PMID 8942976 JRNL DOI 10.1073/PNAS.93.24.13577 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 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 : 9726 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) : 0.212 REMARK 3 FREE R VALUE : 0.330 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 : 904 REMARK 3 NUCLEIC ACID ATOMS : 814 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 87 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) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 2.070 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 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: LOCAL SCALING OF F(OBSERVED) AGAINST REMARK 3 F(CALCULATED) WITH LSCALE (AUTHOR: M. ROULD) TO CORRECT FOR REMARK 3 ANISOTROPIC DIFFRACTION AND ABSORPTION EFFECTS REMARK 4 REMARK 4 1UBD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000176902. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-95 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B 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 : 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 : 12347 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.08000 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 (%): 60.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.55000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.55000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.85000 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: A, B, C 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 C 291 REMARK 465 GLU C 292 REMARK 465 PRO C 293 REMARK 465 ARG C 294 REMARK 465 LYS C 409 REMARK 465 ALA C 410 REMARK 465 LYS C 411 REMARK 465 ASN C 412 REMARK 465 ASN C 413 REMARK 465 GLN C 414 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 C 295 OG1 CG2 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 A 7 C5 DT A 7 C7 0.052 REMARK 500 DT A 11 C5 DT A 11 C7 0.039 REMARK 500 DG B 22 P DG B 22 O5' 0.063 REMARK 500 DG B 22 C5' DG B 22 C4' 0.049 REMARK 500 DA B 29 O3' DA B 29 C3' -0.057 REMARK 500 DA B 29 O3' DA B 30 P -0.077 REMARK 500 DA B 30 C6 DA B 30 N1 -0.048 REMARK 500 DT B 31 C5 DT B 31 C7 0.042 REMARK 500 DC B 38 C5' DC B 38 C4' 0.055 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 DA A 1 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC A 6 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 8 C1' - O4' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT A 12 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT A 12 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES REMARK 500 DT A 14 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA A 16 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA A 17 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 DG A 18 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DC A 19 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 19 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 7.5 DEGREES REMARK 500 DT B 24 O4' - C1' - N1 ANGL. DEV. = 7.3 DEGREES REMARK 500 DT B 25 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 25 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 DC B 26 C1' - O4' - C4' ANGL. DEV. = -9.1 DEGREES REMARK 500 DA B 27 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 28 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA B 29 O4' - C1' - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 DA B 30 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 DT B 31 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 DT B 31 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT B 31 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG B 32 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 33 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DA B 34 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 35 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 DG B 35 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 DA B 36 C3' - O3' - P ANGL. DEV. = 10.0 DEGREES REMARK 500 DC B 37 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 38 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DC B 38 O4' - C1' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 DC B 38 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 DC B 39 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DT B 40 O4' - C1' - N1 ANGL. DEV. = 9.1 DEGREES REMARK 500 DT B 40 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 PRO C 352 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG C 363 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG C 363 NE - CZ - NH2 ANGL. DEV. = -4.4 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 PRO C 299 -72.05 -48.32 REMARK 500 HIS C 300 111.16 -8.92 REMARK 500 LYS C 301 -84.45 -16.55 REMARK 500 CYS C 360 -90.35 -86.33 REMARK 500 ASP C 380 91.66 -59.04 REMARK 500 TYR C 383 77.94 -112.72 REMARK 500 ASP C 388 108.00 -53.71 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 DA A 1 0.07 SIDE CHAIN REMARK 500 DC B 38 0.07 SIDE CHAIN REMARK 500 DT B 40 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 C 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 298 SG REMARK 620 2 CYS C 303 SG 110.4 REMARK 620 3 HIS C 316 NE2 106.9 109.3 REMARK 620 4 HIS C 320 NE2 109.1 110.9 110.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 327 SG REMARK 620 2 CYS C 330 SG 112.6 REMARK 620 3 HIS C 343 NE2 108.7 107.2 REMARK 620 4 HIS C 347 NE2 108.7 111.6 107.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 355 SG REMARK 620 2 CYS C 360 SG 110.2 REMARK 620 3 HIS C 373 NE2 115.3 107.8 REMARK 620 4 HIS C 377 NE2 105.5 110.9 107.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 385 SG REMARK 620 2 CYS C 390 SG 106.5 REMARK 620 3 HIS C 403 NE2 111.8 113.9 REMARK 620 4 HIS C 407 NE2 108.4 109.1 107.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 504 DBREF 1UBD C 291 414 UNP P25490 TYY1_HUMAN 293 414 DBREF 1UBD A 1 20 PDB 1UBD 1UBD 1 20 DBREF 1UBD B 21 40 PDB 1UBD 1UBD 21 40 SEQADV 1UBD MET C 291 UNP P25490 ASP 291 ENGINEERED MUTATION SEQADV 1UBD GLU C 292 UNP P25490 ALA 292 ENGINEERED MUTATION SEQRES 1 A 20 DA DG DG DG DT DC DT DC DC DA DT DT DT SEQRES 2 A 20 DT DG DA DA DG DC DG SEQRES 1 B 20 DC DG DC DT DT DC DA DA DA DA DT DG DG SEQRES 2 B 20 DA DG DA DC DC DC DT SEQRES 1 C 124 MET GLU PRO ARG THR ILE ALA CYS PRO HIS LYS GLY CYS SEQRES 2 C 124 THR LYS MET PHE ARG ASP ASN SER ALA MET ARG LYS HIS SEQRES 3 C 124 LEU HIS THR HIS GLY PRO ARG VAL HIS VAL CYS ALA GLU SEQRES 4 C 124 CYS GLY LYS ALA PHE VAL GLU SER SER LYS LEU LYS ARG SEQRES 5 C 124 HIS GLN LEU VAL HIS THR GLY GLU LYS PRO PHE GLN CYS SEQRES 6 C 124 THR PHE GLU GLY CYS GLY LYS ARG PHE SER LEU ASP PHE SEQRES 7 C 124 ASN LEU ARG THR HIS VAL ARG ILE HIS THR GLY ASP ARG SEQRES 8 C 124 PRO TYR VAL CYS PRO PHE ASP GLY CYS ASN LYS LYS PHE SEQRES 9 C 124 ALA GLN SER THR ASN LEU LYS SER HIS ILE LEU THR HIS SEQRES 10 C 124 ALA LYS ALA LYS ASN ASN GLN HET ZN C 501 1 HET ZN C 502 1 HET ZN C 503 1 HET ZN C 504 1 HETNAM ZN ZINC ION FORMUL 4 ZN 4(ZN 2+) FORMUL 8 HOH *87(H2 O) HELIX 1 1 ASN C 310 HIS C 320 1 11 HELIX 2 2 SER C 337 VAL C 346 1 10 HELIX 3 3 ASP C 367 THR C 378 1 12 HELIX 4 4 LYS C 401 THR C 406 1 6 SHEET 1 A 2 ILE C 296 ALA C 297 0 SHEET 2 A 2 MET C 306 PHE C 307 -1 N PHE C 307 O ILE C 296 SHEET 1 B 2 HIS C 325 VAL C 326 0 SHEET 2 B 2 ALA C 333 PHE C 334 -1 N PHE C 334 O HIS C 325 SHEET 1 C 2 PHE C 353 GLN C 354 0 SHEET 2 C 2 ARG C 363 PHE C 364 -1 N PHE C 364 O PHE C 353 LINK SG CYS C 298 ZN ZN C 501 1555 1555 2.33 LINK SG CYS C 303 ZN ZN C 501 1555 1555 2.32 LINK NE2 HIS C 316 ZN ZN C 501 1555 1555 2.00 LINK NE2 HIS C 320 ZN ZN C 501 1555 1555 2.01 LINK SG CYS C 327 ZN ZN C 502 1555 1555 2.28 LINK SG CYS C 330 ZN ZN C 502 1555 1555 2.31 LINK NE2 HIS C 343 ZN ZN C 502 1555 1555 2.04 LINK NE2 HIS C 347 ZN ZN C 502 1555 1555 2.01 LINK SG CYS C 355 ZN ZN C 503 1555 1555 2.29 LINK SG CYS C 360 ZN ZN C 503 1555 1555 2.29 LINK NE2 HIS C 373 ZN ZN C 503 1555 1555 2.00 LINK NE2 HIS C 377 ZN ZN C 503 1555 1555 2.00 LINK SG CYS C 385 ZN ZN C 504 1555 1555 2.32 LINK SG CYS C 390 ZN ZN C 504 1555 1555 2.36 LINK NE2 HIS C 403 ZN ZN C 504 1555 1555 2.01 LINK NE2 HIS C 407 ZN ZN C 504 1555 1555 2.02 SITE 1 AC1 4 CYS C 298 CYS C 303 HIS C 316 HIS C 320 SITE 1 AC2 4 CYS C 327 CYS C 330 HIS C 343 HIS C 347 SITE 1 AC3 4 CYS C 355 CYS C 360 HIS C 373 HIS C 377 SITE 1 AC4 4 CYS C 385 CYS C 390 HIS C 403 HIS C 407 CRYST1 44.000 65.700 117.100 90.00 90.00 90.00 P 21 21 21 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 0.022727 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015221 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008540 0.00000