HEADER HYDROLASE 31-MAR-06 2GK7 TITLE STRUCTURAL AND FUNCTIONAL INSIGHTS INTO THE HUMAN UPF1 HELICASE CORE COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATOR OF NONSENSE TRANSCRIPTS 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HELICASE CORE DOMAIN(RESIDUES 295-914); COMPND 5 SYNONYM: ATP-DEPENDENT HELICASE RENT1, NONSENSE MRNA REDUCING FACTOR COMPND 6 1, NORF1, UP-FRAMESHIFT SUPPRESSOR 1 HOMOLOG, HUPF1; COMPND 7 EC: 3.6.1.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL-21 STAR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS UPF1, HELICASE, NMD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.CHENG,D.MUHLRAD,R.PARKER,H.SONG REVDAT 5 25-OCT-23 2GK7 1 REMARK SEQADV REVDAT 4 13-JUL-11 2GK7 1 VERSN REVDAT 3 24-FEB-09 2GK7 1 VERSN REVDAT 2 23-JAN-07 2GK7 1 JRNL REVDAT 1 09-JAN-07 2GK7 0 JRNL AUTH Z.CHENG,D.MUHLRAD,M.K.LIM,R.PARKER,H.SONG JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS INTO THE HUMAN UPF1 JRNL TITL 2 HELICASE CORE JRNL REF EMBO J. V. 26 253 2007 JRNL REFN ISSN 0261-4189 JRNL PMID 17159905 JRNL DOI 10.1038/SJ.EMBOJ.7601464 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21121 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) : 0.260 REMARK 3 R VALUE (WORKING SET) : 0.258 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1138 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1529 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3850 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.4480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4719 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 58 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.80000 REMARK 3 B22 (A**2) : 1.80000 REMARK 3 B33 (A**2) : -3.61000 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): 1.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.404 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.394 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 43.334 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.908 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4808 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6499 ; 1.294 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 591 ; 6.576 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 219 ;37.393 ;24.292 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 868 ;20.702 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;20.024 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 728 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3596 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2342 ; 0.236 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3276 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 165 ; 0.154 ; 0.200 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): 50 ; 0.228 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.225 ; 0.200 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): 3031 ; 0.462 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4794 ; 0.820 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1977 ; 1.026 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1705 ; 1.763 ; 4.500 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): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 295 A 324 REMARK 3 RESIDUE RANGE : A 325 A 415 REMARK 3 RESIDUE RANGE : A 416 A 699 REMARK 3 RESIDUE RANGE : A 700 A 908 REMARK 3 ORIGIN FOR THE GROUP (A): 75.0070 33.9750 6.8122 REMARK 3 T TENSOR REMARK 3 T11: 0.0220 T22: -0.2115 REMARK 3 T33: -0.1408 T12: 0.4696 REMARK 3 T13: -0.3481 T23: -0.1176 REMARK 3 L TENSOR REMARK 3 L11: 2.5339 L22: 1.8021 REMARK 3 L33: 1.4307 L12: -0.1277 REMARK 3 L13: -0.1690 L23: 0.0242 REMARK 3 S TENSOR REMARK 3 S11: -0.5790 S12: -0.1715 S13: 0.5030 REMARK 3 S21: 0.0953 S22: 0.3034 S23: 0.1484 REMARK 3 S31: -0.2940 S32: -0.4489 S33: 0.2755 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 REMARK 4 REMARK 4 2GK7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037220. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : GRAPHATE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24896 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 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 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT, SAD REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 2GJK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM NA/K PHOSPHATE, 6-8% PEG3350, REMARK 280 10MM DTT, PH 5.8, EVAPORATION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 22.72900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 97.59450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 97.59450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.09350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 97.59450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 97.59450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.36450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 97.59450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 97.59450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.09350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 97.59450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 97.59450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 11.36450 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 22.72900 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: MONOMERIC 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 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 PRO A 291 REMARK 465 LEU A 292 REMARK 465 GLY A 293 REMARK 465 SER A 294 REMARK 465 LEU A 337 REMARK 465 ASN A 338 REMARK 465 LYS A 367 REMARK 465 GLY A 368 REMARK 465 ASP A 369 REMARK 465 LEU A 370 REMARK 465 ALA A 371 REMARK 465 PRO A 372 REMARK 465 LEU A 373 REMARK 465 ALA A 401 REMARK 465 PRO A 402 REMARK 465 VAL A 403 REMARK 465 GLU A 404 REMARK 465 VAL A 405 REMARK 465 THR A 584 REMARK 465 GLY A 585 REMARK 465 GLU A 586 REMARK 465 LEU A 587 REMARK 465 SER A 909 REMARK 465 LEU A 910 REMARK 465 MET A 911 REMARK 465 GLN A 912 REMARK 465 PHE A 913 REMARK 465 SER A 914 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 GLY A 791 C GLY A 791 O -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 GLY A 791 O - C - N ANGL. DEV. = 11.5 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 TYR A 296 -169.18 -68.91 REMARK 500 ASP A 334 -151.25 -116.83 REMARK 500 LYS A 340 77.61 -101.90 REMARK 500 ILE A 342 -69.74 -154.25 REMARK 500 PRO A 348 119.73 -37.94 REMARK 500 SER A 352 -155.52 -159.51 REMARK 500 ARG A 365 -109.61 -101.86 REMARK 500 ILE A 377 -137.40 -94.06 REMARK 500 PRO A 384 126.48 -29.13 REMARK 500 ASN A 386 13.82 -59.81 REMARK 500 TYR A 387 57.36 -116.77 REMARK 500 ASP A 389 99.90 -46.21 REMARK 500 SER A 398 56.13 15.71 REMARK 500 VAL A 399 81.75 44.75 REMARK 500 HIS A 407 10.85 -155.86 REMARK 500 PHE A 409 -165.46 -112.16 REMARK 500 GLN A 466 -93.77 8.54 REMARK 500 ASN A 514 71.93 171.18 REMARK 500 GLU A 573 -60.36 72.14 REMARK 500 ASP A 582 86.23 -66.54 REMARK 500 SER A 589 -87.53 -121.83 REMARK 500 ASP A 662 113.94 -174.71 REMARK 500 LEU A 666 120.47 -33.28 REMARK 500 GLU A 718 51.74 38.70 REMARK 500 LYS A 733 99.40 -58.58 REMARK 500 ASP A 736 52.07 -115.42 REMARK 500 PRO A 745 46.76 -72.43 REMARK 500 GLN A 752 54.91 -112.17 REMARK 500 SER A 825 -177.98 -66.70 REMARK 500 ASN A 845 -35.74 -145.25 REMARK 500 GLU A 846 -11.83 67.87 REMARK 500 GLN A 882 105.62 172.56 REMARK 500 PRO A 883 -32.20 -35.51 REMARK 500 LEU A 898 111.09 172.78 REMARK 500 LEU A 903 61.32 73.89 REMARK 500 ASN A 904 -163.05 -125.15 REMARK 500 LEU A 906 164.60 -47.75 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 GLY A 513 ASN A 514 -144.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 990 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GJK RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH ANP(5'-ADENYL-IMIDO-TRIPHOSPHATE) REMARK 900 RELATED ID: 2GK6 RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH ADP(ADENOSINE-5'-DIPHOSPHATE) REMARK 900 RELATED ID: 2GK8 RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH SAP(ADENOSINE-5'-DIPHOSPHATE REMARK 900 MONOTHIOPHOSPHATE) DBREF 2GK7 A 295 914 UNP Q92900 RENT1_HUMAN 295 914 SEQADV 2GK7 PRO A 291 UNP Q92900 CLONING ARTIFACT SEQADV 2GK7 LEU A 292 UNP Q92900 CLONING ARTIFACT SEQADV 2GK7 GLY A 293 UNP Q92900 CLONING ARTIFACT SEQADV 2GK7 SER A 294 UNP Q92900 CLONING ARTIFACT SEQRES 1 A 624 PRO LEU GLY SER ARG TYR GLU ASP ALA TYR GLN TYR GLN SEQRES 2 A 624 ASN ILE PHE GLY PRO LEU VAL LYS LEU GLU ALA ASP TYR SEQRES 3 A 624 ASP LYS LYS LEU LYS GLU SER GLN THR GLN ASP ASN ILE SEQRES 4 A 624 THR VAL ARG TRP ASP LEU GLY LEU ASN LYS LYS ARG ILE SEQRES 5 A 624 ALA TYR PHE THR LEU PRO LYS THR ASP SER ASP MET ARG SEQRES 6 A 624 LEU MET GLN GLY ASP GLU ILE CYS LEU ARG TYR LYS GLY SEQRES 7 A 624 ASP LEU ALA PRO LEU TRP LYS GLY ILE GLY HIS VAL ILE SEQRES 8 A 624 LYS VAL PRO ASP ASN TYR GLY ASP GLU ILE ALA ILE GLU SEQRES 9 A 624 LEU ARG SER SER VAL GLY ALA PRO VAL GLU VAL THR HIS SEQRES 10 A 624 ASN PHE GLN VAL ASP PHE VAL TRP LYS SER THR SER PHE SEQRES 11 A 624 ASP ARG MET GLN SER ALA LEU LYS THR PHE ALA VAL ASP SEQRES 12 A 624 GLU THR SER VAL SER GLY TYR ILE TYR HIS LYS LEU LEU SEQRES 13 A 624 GLY HIS GLU VAL GLU ASP VAL ILE ILE LYS CYS GLN LEU SEQRES 14 A 624 PRO LYS ARG PHE THR ALA GLN GLY LEU PRO ASP LEU ASN SEQRES 15 A 624 HIS SER GLN VAL TYR ALA VAL LYS THR VAL LEU GLN ARG SEQRES 16 A 624 PRO LEU SER LEU ILE GLN GLY PRO PRO GLY THR GLY LYS SEQRES 17 A 624 THR VAL THR SER ALA THR ILE VAL TYR HIS LEU ALA ARG SEQRES 18 A 624 GLN GLY ASN GLY PRO VAL LEU VAL CYS ALA PRO SER ASN SEQRES 19 A 624 ILE ALA VAL ASP GLN LEU THR GLU LYS ILE HIS GLN THR SEQRES 20 A 624 GLY LEU LYS VAL VAL ARG LEU CYS ALA LYS SER ARG GLU SEQRES 21 A 624 ALA ILE ASP SER PRO VAL SER PHE LEU ALA LEU HIS ASN SEQRES 22 A 624 GLN ILE ARG ASN MET ASP SER MET PRO GLU LEU GLN LYS SEQRES 23 A 624 LEU GLN GLN LEU LYS ASP GLU THR GLY GLU LEU SER SER SEQRES 24 A 624 ALA ASP GLU LYS ARG TYR ARG ALA LEU LYS ARG THR ALA SEQRES 25 A 624 GLU ARG GLU LEU LEU MET ASN ALA ASP VAL ILE CYS CYS SEQRES 26 A 624 THR CYS VAL GLY ALA GLY ASP PRO ARG LEU ALA LYS MET SEQRES 27 A 624 GLN PHE ARG SER ILE LEU ILE ASP GLU SER THR GLN ALA SEQRES 28 A 624 THR GLU PRO GLU CYS MET VAL PRO VAL VAL LEU GLY ALA SEQRES 29 A 624 LYS GLN LEU ILE LEU VAL GLY ASP HIS CYS GLN LEU GLY SEQRES 30 A 624 PRO VAL VAL MET CYS LYS LYS ALA ALA LYS ALA GLY LEU SEQRES 31 A 624 SER GLN SER LEU PHE GLU ARG LEU VAL VAL LEU GLY ILE SEQRES 32 A 624 ARG PRO ILE ARG LEU GLN VAL GLN TYR ARG MET HIS PRO SEQRES 33 A 624 ALA LEU SER ALA PHE PRO SER ASN ILE PHE TYR GLU GLY SEQRES 34 A 624 SER LEU GLN ASN GLY VAL THR ALA ALA ASP ARG VAL LYS SEQRES 35 A 624 LYS GLY PHE ASP PHE GLN TRP PRO GLN PRO ASP LYS PRO SEQRES 36 A 624 MET PHE PHE TYR VAL THR GLN GLY GLN GLU GLU ILE ALA SEQRES 37 A 624 SER SER GLY THR SER TYR LEU ASN ARG THR GLU ALA ALA SEQRES 38 A 624 ASN VAL GLU LYS ILE THR THR LYS LEU LEU LYS ALA GLY SEQRES 39 A 624 ALA LYS PRO ASP GLN ILE GLY ILE ILE THR PRO TYR GLU SEQRES 40 A 624 GLY GLN ARG SER TYR LEU VAL GLN TYR MET GLN PHE SER SEQRES 41 A 624 GLY SER LEU HIS THR LYS LEU TYR GLN GLU VAL GLU ILE SEQRES 42 A 624 ALA SER VAL ASP ALA PHE GLN GLY ARG GLU LYS ASP PHE SEQRES 43 A 624 ILE ILE LEU SER CYS VAL ARG ALA ASN GLU HIS GLN GLY SEQRES 44 A 624 ILE GLY PHE LEU ASN ASP PRO ARG ARG LEU ASN VAL ALA SEQRES 45 A 624 LEU THR ARG ALA ARG TYR GLY VAL ILE ILE VAL GLY ASN SEQRES 46 A 624 PRO LYS ALA LEU SER LYS GLN PRO LEU TRP ASN HIS LEU SEQRES 47 A 624 LEU ASN TYR TYR LYS GLU GLN LYS VAL LEU VAL GLU GLY SEQRES 48 A 624 PRO LEU ASN ASN LEU ARG GLU SER LEU MET GLN PHE SER HET PO4 A 990 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *58(H2 O) HELIX 1 1 ASP A 298 GLU A 322 1 25 HELIX 2 2 SER A 417 ASP A 433 1 17 HELIX 3 3 SER A 438 LEU A 446 1 9 HELIX 4 4 ASN A 472 LEU A 483 1 12 HELIX 5 5 GLY A 497 GLN A 512 1 16 HELIX 6 6 SER A 523 GLN A 536 1 14 HELIX 7 7 ALA A 546 GLU A 550 5 5 HELIX 8 8 VAL A 556 LEU A 559 5 4 HELIX 9 9 ALA A 560 ASN A 567 1 8 HELIX 10 10 GLU A 573 ASP A 582 1 10 HELIX 11 11 SER A 589 ALA A 610 1 22 HELIX 12 12 VAL A 618 ALA A 626 5 9 HELIX 13 13 GLU A 637 ALA A 641 5 5 HELIX 14 14 THR A 642 VAL A 651 1 10 HELIX 15 15 CYS A 672 GLY A 679 1 8 HELIX 16 16 SER A 683 LEU A 691 1 9 HELIX 17 17 HIS A 705 TYR A 717 1 13 HELIX 18 18 ALA A 727 VAL A 731 5 5 HELIX 19 19 ARG A 767 GLY A 784 1 18 HELIX 20 20 LYS A 786 ASP A 788 5 3 HELIX 21 21 TYR A 796 SER A 810 1 15 HELIX 22 22 HIS A 814 GLN A 819 1 6 HELIX 23 23 VAL A 826 GLN A 830 5 5 HELIX 24 24 ASP A 855 THR A 864 1 10 HELIX 25 25 ASN A 875 SER A 880 1 6 HELIX 26 26 GLN A 882 GLN A 895 1 14 SHEET 1 A 2 ILE A 362 LEU A 364 0 SHEET 2 A 2 VAL A 411 PHE A 413 -1 O ASP A 412 N CYS A 363 SHEET 1 B 2 HIS A 379 LYS A 382 0 SHEET 2 B 2 ALA A 392 GLU A 394 -1 O ALA A 392 N ILE A 381 SHEET 1 C 7 VAL A 541 ARG A 543 0 SHEET 2 C 7 VAL A 612 THR A 616 1 O CYS A 614 N VAL A 542 SHEET 3 C 7 VAL A 517 ALA A 521 1 N VAL A 519 O ILE A 613 SHEET 4 C 7 SER A 632 ILE A 635 1 O SER A 632 N LEU A 518 SHEET 5 C 7 GLN A 656 GLY A 661 1 O VAL A 660 N ILE A 635 SHEET 6 C 7 LEU A 487 GLN A 491 1 N SER A 488 O LEU A 659 SHEET 7 C 7 ILE A 696 ARG A 697 1 O ILE A 696 N LEU A 489 SHEET 1 D 2 VAL A 700 GLN A 701 0 SHEET 2 D 2 GLN A 722 ASN A 723 1 O GLN A 722 N GLN A 701 SHEET 1 E 5 MET A 746 VAL A 750 0 SHEET 2 E 5 ALA A 866 GLY A 874 1 O ILE A 872 N TYR A 749 SHEET 3 E 5 LYS A 834 SER A 840 1 N ILE A 837 O ILE A 871 SHEET 4 E 5 ILE A 790 ILE A 793 1 N ILE A 793 O ILE A 838 SHEET 5 E 5 GLU A 822 ALA A 824 1 O ALA A 824 N ILE A 792 SHEET 1 F 2 GLU A 755 ILE A 757 0 SHEET 2 F 2 TYR A 764 ASN A 766 -1 O LEU A 765 N GLU A 756 CISPEP 1 ALA A 343 TYR A 344 0 -10.21 CISPEP 2 THR A 406 HIS A 407 0 -4.39 SITE 1 AC1 9 HOH A 6 HOH A 34 PRO A 494 GLY A 495 SITE 2 AC1 9 LYS A 498 GLN A 665 ARG A 703 GLY A 831 SITE 3 AC1 9 ARG A 865 CRYST1 195.189 195.189 45.458 90.00 90.00 90.00 P 43 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 0.005123 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021998 0.00000