HEADER HYDROLASE 03-AUG-21 7PCP TITLE CRYSTAL STRUCTURE OF CD73 IN COMPLEX WITH 5-IODOURACIL IN THE OPEN TITLE 2 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-NUCLEOTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5'-NT,ECTO-5'-NUCLEOTIDASE; COMPND 5 EC: 3.1.3.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NT5E, NT5, NTE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ECTO-5'-NUCLEOTIDASE, EN, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.R.SCALETTI,N.STRATER REVDAT 3 31-JAN-24 7PCP 1 REMARK REVDAT 2 29-DEC-21 7PCP 1 JRNL REVDAT 1 13-OCT-21 7PCP 0 JRNL AUTH E.SCALETTI,F.U.HUSCHMANN,U.MUELLER,M.S.WEISS,N.STRATER JRNL TITL SUBSTRATE BINDING MODES OF PURINE AND PYRIMIDINE NUCLEOTIDES JRNL TITL 2 TO HUMAN ECTO-5'-NUCLEOTIDASE (CD73) AND INHIBITION BY THEIR JRNL TITL 3 BISPHOSPHONIC ACID DERIVATIVES. JRNL REF PURINERGIC SIGNAL V. 17 693 2021 JRNL REFN ISSN 1573-9546 JRNL PMID 34403084 JRNL DOI 10.1007/S11302-021-09802-W REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 114949 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) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6109 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) : 1.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8305 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE SET COUNT : 427 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4076 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 479 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.58000 REMARK 3 B22 (A**2) : -0.11000 REMARK 3 B33 (A**2) : 0.69000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.045 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.048 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.035 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.058 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4404 ; 0.014 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4182 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6024 ; 1.873 ; 1.634 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9682 ; 1.538 ; 1.580 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 585 ; 9.041 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 220 ;34.409 ;23.318 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 760 ;11.924 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;16.855 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 571 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5117 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 991 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 8586 ; 3.353 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7PCP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1292117487. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 122396 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.377 REMARK 200 RESOLUTION RANGE LOW (A) : 47.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.76800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4H2G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7 MG/ML PROTEIN CONCENTRATION, 100 MM REMARK 280 TRIS PH 7.8, 10 % PEG6000, EQUAL AMOUNTS OF PROTEIN AND REMARK 280 RESERVOIR. FOLLOWING CRYSTAL FORMATION (1-2 DAYS), THE CRYSTALS REMARK 280 WERE TRANSFERRED TO SOAKING SOLUTION CONTAINING RESERVOIR REMARK 280 SOLUTION AND 10 MM 5-IODOURACIL. CRYSTALS WERE THEN TRANSFERRED REMARK 280 TO CRYO SOLUTION CONTAINING AN ADDITIONAL 20 % GLYCEROL, SOAKED REMARK 280 FOR ~2-5 MIN, AND FLASH FROZEN IN LIQUID NITROGEN., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 292K 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 33.61000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 65.91000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.61000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 65.91000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -186.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 67.22000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1108 LIES ON A SPECIAL POSITION. 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 4 REMARK 465 ALA A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 HIS A 11 REMARK 465 VAL A 12 REMARK 465 GLY A 13 REMARK 465 THR A 14 REMARK 465 GLY A 15 REMARK 465 SER A 16 REMARK 465 ASN A 17 REMARK 465 ASP A 18 REMARK 465 ASP A 19 REMARK 465 ASP A 20 REMARK 465 ASP A 21 REMARK 465 LYS A 22 REMARK 465 SER A 23 REMARK 465 PRO A 24 REMARK 465 ASP A 25 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 A 296 CG CD OE1 OE2 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 GLU A 543 CD GLU A 543 OE2 -0.069 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 TYR A 87 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 TYR A 87 CB - CG - CD1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 395 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 395 NE - CZ - NH2 ANGL. DEV. = 7.0 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 GLN A 88 128.04 77.18 REMARK 500 SER A 141 116.77 -168.03 REMARK 500 SER A 185 -165.93 -171.01 REMARK 500 HIS A 243 -49.19 81.09 REMARK 500 SER A 255 -150.45 -142.79 REMARK 500 TYR A 281 -122.92 58.87 REMARK 500 ASN A 306 149.00 -179.05 REMARK 500 SER A 352 -60.35 -90.13 REMARK 500 ASP A 377 -158.71 -82.92 REMARK 500 ASN A 402 55.96 -90.35 REMARK 500 LYS A 536 -51.27 75.35 REMARK 500 TYR A 539 53.19 -153.98 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 GLU A 129 PRO A 130 38.98 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 GLU A 129 10.39 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 A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 36 OD1 REMARK 620 2 HIS A 38 NE2 116.4 REMARK 620 3 ASP A 85 OD2 93.2 93.1 REMARK 620 4 HOH A 742 O 97.7 144.6 75.1 REMARK 620 5 HOH A 748 O 97.4 90.7 165.8 94.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 85 OD2 REMARK 620 2 ASN A 117 OD1 95.8 REMARK 620 3 HIS A 220 NE2 89.3 94.9 REMARK 620 4 HIS A 243 ND1 169.4 91.3 98.0 REMARK 620 5 HOH A 742 O 76.9 135.6 128.1 92.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 603 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 213 O REMARK 620 2 ASP A 237 OD1 136.1 REMARK 620 3 ASP A 237 OD2 83.9 53.4 REMARK 620 4 GLY A 298 O 83.4 89.1 93.6 REMARK 620 5 HOH A 738 O 84.9 100.0 86.0 168.3 REMARK 620 6 HOH A 986 O 79.9 142.2 163.8 83.9 93.2 REMARK 620 7 HOH A1020 O 149.4 73.9 126.7 92.7 96.9 69.5 REMARK 620 N 1 2 3 4 5 6 DBREF 7PCP A 27 549 UNP P21589 5NTD_HUMAN 27 549 SEQADV 7PCP MET A 4 UNP P21589 INITIATING METHIONINE SEQADV 7PCP ALA A 5 UNP P21589 EXPRESSION TAG SEQADV 7PCP HIS A 6 UNP P21589 EXPRESSION TAG SEQADV 7PCP HIS A 7 UNP P21589 EXPRESSION TAG SEQADV 7PCP HIS A 8 UNP P21589 EXPRESSION TAG SEQADV 7PCP HIS A 9 UNP P21589 EXPRESSION TAG SEQADV 7PCP HIS A 10 UNP P21589 EXPRESSION TAG SEQADV 7PCP HIS A 11 UNP P21589 EXPRESSION TAG SEQADV 7PCP VAL A 12 UNP P21589 EXPRESSION TAG SEQADV 7PCP GLY A 13 UNP P21589 EXPRESSION TAG SEQADV 7PCP THR A 14 UNP P21589 EXPRESSION TAG SEQADV 7PCP GLY A 15 UNP P21589 EXPRESSION TAG SEQADV 7PCP SER A 16 UNP P21589 EXPRESSION TAG SEQADV 7PCP ASN A 17 UNP P21589 EXPRESSION TAG SEQADV 7PCP ASP A 18 UNP P21589 EXPRESSION TAG SEQADV 7PCP ASP A 19 UNP P21589 EXPRESSION TAG SEQADV 7PCP ASP A 20 UNP P21589 EXPRESSION TAG SEQADV 7PCP ASP A 21 UNP P21589 EXPRESSION TAG SEQADV 7PCP LYS A 22 UNP P21589 EXPRESSION TAG SEQADV 7PCP SER A 23 UNP P21589 EXPRESSION TAG SEQADV 7PCP PRO A 24 UNP P21589 EXPRESSION TAG SEQADV 7PCP ASP A 25 UNP P21589 EXPRESSION TAG SEQADV 7PCP PRO A 26 UNP P21589 EXPRESSION TAG SEQADV 7PCP ASP A 53 UNP P21589 ASN 53 ENGINEERED MUTATION SEQADV 7PCP SER A 145 UNP P21589 LYS 145 ENGINEERED MUTATION SEQADV 7PCP SER A 147 UNP P21589 LYS 147 ENGINEERED MUTATION SEQADV 7PCP ASP A 311 UNP P21589 ASN 311 ENGINEERED MUTATION SEQADV 7PCP ASP A 333 UNP P21589 ASN 333 ENGINEERED MUTATION SEQADV 7PCP ALA A 376 UNP P21589 THR 376 VARIANT SEQADV 7PCP ASP A 403 UNP P21589 ASN 403 ENGINEERED MUTATION SEQADV 7PCP SER A 478 UNP P21589 LYS 478 ENGINEERED MUTATION SEQRES 1 A 546 MET ALA HIS HIS HIS HIS HIS HIS VAL GLY THR GLY SER SEQRES 2 A 546 ASN ASP ASP ASP ASP LYS SER PRO ASP PRO TRP GLU LEU SEQRES 3 A 546 THR ILE LEU HIS THR ASN ASP VAL HIS SER ARG LEU GLU SEQRES 4 A 546 GLN THR SER GLU ASP SER SER LYS CYS VAL ASP ALA SER SEQRES 5 A 546 ARG CYS MET GLY GLY VAL ALA ARG LEU PHE THR LYS VAL SEQRES 6 A 546 GLN GLN ILE ARG ARG ALA GLU PRO ASN VAL LEU LEU LEU SEQRES 7 A 546 ASP ALA GLY ASP GLN TYR GLN GLY THR ILE TRP PHE THR SEQRES 8 A 546 VAL TYR LYS GLY ALA GLU VAL ALA HIS PHE MET ASN ALA SEQRES 9 A 546 LEU ARG TYR ASP ALA MET ALA LEU GLY ASN HIS GLU PHE SEQRES 10 A 546 ASP ASN GLY VAL GLU GLY LEU ILE GLU PRO LEU LEU LYS SEQRES 11 A 546 GLU ALA LYS PHE PRO ILE LEU SER ALA ASN ILE SER ALA SEQRES 12 A 546 SER GLY PRO LEU ALA SER GLN ILE SER GLY LEU TYR LEU SEQRES 13 A 546 PRO TYR LYS VAL LEU PRO VAL GLY ASP GLU VAL VAL GLY SEQRES 14 A 546 ILE VAL GLY TYR THR SER LYS GLU THR PRO PHE LEU SER SEQRES 15 A 546 ASN PRO GLY THR ASN LEU VAL PHE GLU ASP GLU ILE THR SEQRES 16 A 546 ALA LEU GLN PRO GLU VAL ASP LYS LEU LYS THR LEU ASN SEQRES 17 A 546 VAL ASN LYS ILE ILE ALA LEU GLY HIS SER GLY PHE GLU SEQRES 18 A 546 MET ASP LYS LEU ILE ALA GLN LYS VAL ARG GLY VAL ASP SEQRES 19 A 546 VAL VAL VAL GLY GLY HIS SER ASN THR PHE LEU TYR THR SEQRES 20 A 546 GLY ASN PRO PRO SER LYS GLU VAL PRO ALA GLY LYS TYR SEQRES 21 A 546 PRO PHE ILE VAL THR SER ASP ASP GLY ARG LYS VAL PRO SEQRES 22 A 546 VAL VAL GLN ALA TYR ALA PHE GLY LYS TYR LEU GLY TYR SEQRES 23 A 546 LEU LYS ILE GLU PHE ASP GLU ARG GLY ASN VAL ILE SER SEQRES 24 A 546 SER HIS GLY ASN PRO ILE LEU LEU ASP SER SER ILE PRO SEQRES 25 A 546 GLU ASP PRO SER ILE LYS ALA ASP ILE ASN LYS TRP ARG SEQRES 26 A 546 ILE LYS LEU ASP ASP TYR SER THR GLN GLU LEU GLY LYS SEQRES 27 A 546 THR ILE VAL TYR LEU ASP GLY SER SER GLN SER CYS ARG SEQRES 28 A 546 PHE ARG GLU CYS ASN MET GLY ASN LEU ILE CYS ASP ALA SEQRES 29 A 546 MET ILE ASN ASN ASN LEU ARG HIS ALA ASP GLU MET PHE SEQRES 30 A 546 TRP ASN HIS VAL SER MET CYS ILE LEU ASN GLY GLY GLY SEQRES 31 A 546 ILE ARG SER PRO ILE ASP GLU ARG ASN ASP GLY THR ILE SEQRES 32 A 546 THR TRP GLU ASN LEU ALA ALA VAL LEU PRO PHE GLY GLY SEQRES 33 A 546 THR PHE ASP LEU VAL GLN LEU LYS GLY SER THR LEU LYS SEQRES 34 A 546 LYS ALA PHE GLU HIS SER VAL HIS ARG TYR GLY GLN SER SEQRES 35 A 546 THR GLY GLU PHE LEU GLN VAL GLY GLY ILE HIS VAL VAL SEQRES 36 A 546 TYR ASP LEU SER ARG LYS PRO GLY ASP ARG VAL VAL LYS SEQRES 37 A 546 LEU ASP VAL LEU CYS THR SER CYS ARG VAL PRO SER TYR SEQRES 38 A 546 ASP PRO LEU LYS MET ASP GLU VAL TYR LYS VAL ILE LEU SEQRES 39 A 546 PRO ASN PHE LEU ALA ASN GLY GLY ASP GLY PHE GLN MET SEQRES 40 A 546 ILE LYS ASP GLU LEU LEU ARG HIS ASP SER GLY ASP GLN SEQRES 41 A 546 ASP ILE ASN VAL VAL SER THR TYR ILE SER LYS MET LYS SEQRES 42 A 546 VAL ILE TYR PRO ALA VAL GLU GLY ARG ILE LYS PHE SER HET ZN A 601 1 HET ZN A 602 1 HET CA A 603 1 HET DMS A 604 4 HET IUR A 605 9 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM IUR 5-IODOURACIL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 CA CA 2+ FORMUL 5 DMS C2 H6 O S FORMUL 6 IUR C4 H3 I N2 O2 FORMUL 7 HOH *479(H2 O) HELIX 1 AA1 ASP A 53 CYS A 57 5 5 HELIX 2 AA2 GLY A 60 GLU A 75 1 16 HELIX 3 AA3 THR A 90 LYS A 97 1 8 HELIX 4 AA4 GLY A 98 LEU A 108 1 11 HELIX 5 AA5 GLY A 116 ASP A 121 5 6 HELIX 6 AA6 VAL A 124 GLU A 129 1 6 HELIX 7 AA7 SER A 147 SER A 155 1 9 HELIX 8 AA8 GLU A 180 LEU A 184 5 5 HELIX 9 AA9 ASP A 195 LEU A 210 1 16 HELIX 10 AB1 GLY A 222 VAL A 233 1 12 HELIX 11 AB2 ASP A 317 SER A 335 1 19 HELIX 12 AB3 SER A 349 ARG A 354 1 6 HELIX 13 AB4 CYS A 358 ASN A 372 1 15 HELIX 14 AB5 GLY A 392 ILE A 394 5 3 HELIX 15 AB6 TRP A 408 LEU A 415 1 8 HELIX 16 AB7 GLY A 428 HIS A 440 1 13 HELIX 17 AB8 ASN A 499 ASN A 503 1 5 HELIX 18 AB9 GLY A 504 GLY A 507 5 4 HELIX 19 AC1 PHE A 508 LEU A 515 1 8 HELIX 20 AC2 ASP A 524 LYS A 536 1 13 SHEET 1 AA1 6 ILE A 139 LEU A 140 0 SHEET 2 AA1 6 ALA A 112 ALA A 114 1 N MET A 113 O LEU A 140 SHEET 3 AA1 6 VAL A 78 ASP A 82 1 N ASP A 82 O ALA A 114 SHEET 4 AA1 6 TRP A 27 THR A 34 1 N LEU A 32 O LEU A 79 SHEET 5 AA1 6 TYR A 286 PHE A 294 -1 O LEU A 290 N ILE A 31 SHEET 6 AA1 6 VAL A 300 GLY A 305 -1 O HIS A 304 N LYS A 291 SHEET 1 AA2 6 ILE A 139 LEU A 140 0 SHEET 2 AA2 6 ALA A 112 ALA A 114 1 N MET A 113 O LEU A 140 SHEET 3 AA2 6 VAL A 78 ASP A 82 1 N ASP A 82 O ALA A 114 SHEET 4 AA2 6 TRP A 27 THR A 34 1 N LEU A 32 O LEU A 79 SHEET 5 AA2 6 TYR A 286 PHE A 294 -1 O LEU A 290 N ILE A 31 SHEET 6 AA2 6 ILE A 308 LEU A 309 -1 O ILE A 308 N LEU A 287 SHEET 1 AA3 2 ILE A 144 SER A 145 0 SHEET 2 AA3 2 VAL A 192 PHE A 193 -1 O VAL A 192 N SER A 145 SHEET 1 AA4 6 TYR A 161 VAL A 166 0 SHEET 2 AA4 6 GLU A 169 THR A 177 -1 O VAL A 171 N LEU A 164 SHEET 3 AA4 6 ILE A 215 HIS A 220 1 O ILE A 216 N GLY A 172 SHEET 4 AA4 6 VAL A 238 VAL A 240 1 O VAL A 240 N ALA A 217 SHEET 5 AA4 6 LYS A 274 VAL A 278 1 O PRO A 276 N VAL A 239 SHEET 6 AA4 6 PHE A 265 THR A 268 -1 N VAL A 267 O VAL A 275 SHEET 1 AA5 3 THR A 405 THR A 407 0 SHEET 2 AA5 3 GLU A 338 THR A 342 -1 N LEU A 339 O ILE A 406 SHEET 3 AA5 3 VAL A 537 ILE A 538 1 O ILE A 538 N LYS A 341 SHEET 1 AA6 2 CYS A 387 ASN A 390 0 SHEET 2 AA6 2 LEU A 450 GLY A 453 -1 O GLN A 451 N LEU A 389 SHEET 1 AA7 3 VAL A 492 PRO A 498 0 SHEET 2 AA7 3 THR A 420 LYS A 427 -1 N LEU A 426 O TYR A 493 SHEET 3 AA7 3 ARG A 517 GLN A 523 -1 O ASP A 519 N LEU A 423 SHEET 1 AA8 4 TYR A 484 PRO A 486 0 SHEET 2 AA8 4 VAL A 469 LEU A 475 -1 N VAL A 474 O ASP A 485 SHEET 3 AA8 4 ILE A 455 TYR A 459 -1 N HIS A 456 O ASP A 473 SHEET 4 AA8 4 ILE A 546 PHE A 548 1 O LYS A 547 N TYR A 459 SSBOND 1 CYS A 51 CYS A 57 1555 1555 2.08 SSBOND 2 CYS A 353 CYS A 358 1555 1555 2.10 SSBOND 3 CYS A 365 CYS A 387 1555 1555 2.07 SSBOND 4 CYS A 476 CYS A 479 1555 1555 2.06 LINK OD1 ASP A 36 ZN ZN A 602 1555 1555 2.02 LINK NE2 HIS A 38 ZN ZN A 602 1555 1555 2.05 LINK OD2 ASP A 85 ZN ZN A 601 1555 1555 2.20 LINK OD2 ASP A 85 ZN ZN A 602 1555 1555 2.27 LINK OD1 ASN A 117 ZN ZN A 601 1555 1555 2.04 LINK O ASN A 213 CA CA A 603 1555 1555 2.35 LINK NE2 HIS A 220 ZN ZN A 601 1555 1555 2.02 LINK OD1 ASP A 237 CA CA A 603 1555 1555 2.45 LINK OD2 ASP A 237 CA CA A 603 1555 1555 2.50 LINK ND1 HIS A 243 ZN ZN A 601 1555 1555 2.11 LINK O GLY A 298 CA CA A 603 1555 1555 2.43 LINK ZN ZN A 601 O HOH A 742 1555 1555 1.99 LINK ZN ZN A 602 O HOH A 742 1555 1555 1.99 LINK ZN ZN A 602 O HOH A 748 1555 1555 2.11 LINK CA CA A 603 O HOH A 738 1555 1555 2.39 LINK CA CA A 603 O HOH A 986 1555 1555 2.44 LINK CA CA A 603 O HOH A1020 1555 1555 2.43 CISPEP 1 TYR A 263 PRO A 264 0 -12.97 CRYST1 67.220 131.820 66.324 90.00 90.00 90.00 P 21 21 2 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 0.014877 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007586 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015077 0.00000