HEADER TRANSCRIPTION 11-NOV-13 4CEM TITLE CRYSTAL STRUCTURE OF THE FIRST MIF4G DOMAIN OF HUMAN TITLE 2 NONSENSE MEDIATED DECAY FACTOR UPF2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATOR OF NONSENSE TRANSCRIPTS 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MIF4G1, RESIDUES 121-486; COMPND 5 SYNONYM: NONSENSE MRNA REDUCING FACTOR 2, UP-FRAMESHIFT SUPPRESSOR COMPND 6 2 HOMOLOG, HUPF2, UPF2; COMPND 7 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PPROEXHTB KEYWDS TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.CLERICI,A.DENIAUD,V.BOEHM,N.H.GEHRING,C.SCHAFFITZEL, S.CUSACK REVDAT 2 12-MAR-14 4CEM 1 JRNL REVDAT 1 11-DEC-13 4CEM 0 JRNL AUTH M.CLERICI,A.DENIAUD,V.BOEHM,N.H.GEHRING,C.SCHAFFITZEL, JRNL AUTH 2 S.CUSACK JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE THREE MIF4G JRNL TITL 2 DOMAINS OF NONSENSE-MEDIATED DECAY FACTOR UPF2. JRNL REF NUCLEIC ACIDS RES. V. 42 2673 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24271394 JRNL DOI 10.1093/NAR/GKT1197 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0116 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 87.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.89 REMARK 3 NUMBER OF REFLECTIONS : 26788 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) : 0.20761 REMARK 3 R VALUE (WORKING SET) : 0.20532 REMARK 3 FREE R VALUE : 0.25087 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1428 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) : 2.600 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.668 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1942 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.327 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5013 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 54 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.044 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34 REMARK 3 B22 (A**2) : 0.34 REMARK 3 B33 (A**2) : -0.51 REMARK 3 B12 (A**2) : 0.17 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.489 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.290 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.199 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.404 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5159 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3662 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6938 ; 1.059 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8927 ; 0.818 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 615 ; 5.640 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 267 ;33.336 ;24.382 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 984 ;17.829 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;16.339 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 757 ; 0.060 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5651 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1023 ; 0.001 ; 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 : 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 REMARK 3 RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4CEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-NOV-13. REMARK 100 THE PDBE ID CODE IS EBI-58932. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9788 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (MX-225) REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28216 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.60 REMARK 200 RESOLUTION RANGE LOW (A) : 50.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 2.86 REMARK 200 R MERGE (I) : 0.09 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.90 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.37 REMARK 200 R MERGE FOR SHELL (I) : 0.63 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD SHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.8 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BICINE PH 9, 100 MM NACL, REMARK 280 11% PEG 6000 AND AT A PROTEIN CONCENTRATION OF 16 MG/ML REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 105.92000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 52.96000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.44000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.48000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 132.40000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 117 REMARK 465 ALA A 118 REMARK 465 MSE A 119 REMARK 465 GLY A 120 REMARK 465 GLN A 429 REMARK 465 ASP A 430 REMARK 465 LYS A 431 REMARK 465 PRO A 432 REMARK 465 THR A 433 REMARK 465 PRO A 434 REMARK 465 GLU A 435 REMARK 465 GLU A 436 REMARK 465 HIS A 437 REMARK 465 GLY A 438 REMARK 465 PRO A 439 REMARK 465 GLY A 440 REMARK 465 ILE A 441 REMARK 465 ASP A 442 REMARK 465 ILE A 443 REMARK 465 PHE A 444 REMARK 465 THR A 445 REMARK 465 PRO A 446 REMARK 465 GLY A 447 REMARK 465 LYS A 448 REMARK 465 PRO A 449 REMARK 465 GLY A 450 REMARK 465 GLU A 451 REMARK 465 TYR A 452 REMARK 465 ASP A 453 REMARK 465 LEU A 454 REMARK 465 GLU A 455 REMARK 465 GLY A 456 REMARK 465 GLY A 457 REMARK 465 ILE A 458 REMARK 465 TRP A 459 REMARK 465 GLU A 460 REMARK 465 ASP A 461 REMARK 465 GLU A 462 REMARK 465 ASP A 463 REMARK 465 ALA A 464 REMARK 465 ARG A 465 REMARK 465 ASN A 466 REMARK 465 PHE A 467 REMARK 465 TYR A 468 REMARK 465 GLU A 469 REMARK 465 ASN A 470 REMARK 465 LEU A 471 REMARK 465 ILE A 472 REMARK 465 ASP A 473 REMARK 465 LEU A 474 REMARK 465 LYS A 475 REMARK 465 ALA A 476 REMARK 465 PHE A 477 REMARK 465 VAL A 478 REMARK 465 PRO A 479 REMARK 465 ALA A 480 REMARK 465 ILE A 481 REMARK 465 LEU A 482 REMARK 465 PHE A 483 REMARK 465 LYS A 484 REMARK 465 ASP A 485 REMARK 465 ASN A 486 REMARK 465 GLY B 117 REMARK 465 ALA B 118 REMARK 465 MSE B 119 REMARK 465 GLY B 120 REMARK 465 ASP B 430 REMARK 465 LYS B 431 REMARK 465 PRO B 432 REMARK 465 THR B 433 REMARK 465 PRO B 434 REMARK 465 GLU B 435 REMARK 465 GLU B 436 REMARK 465 HIS B 437 REMARK 465 GLY B 438 REMARK 465 PRO B 439 REMARK 465 GLY B 440 REMARK 465 ILE B 441 REMARK 465 ASP B 442 REMARK 465 ILE B 443 REMARK 465 PHE B 444 REMARK 465 THR B 445 REMARK 465 PRO B 446 REMARK 465 GLY B 447 REMARK 465 LYS B 448 REMARK 465 PRO B 449 REMARK 465 GLY B 450 REMARK 465 GLU B 451 REMARK 465 TYR B 452 REMARK 465 ASP B 453 REMARK 465 LEU B 454 REMARK 465 GLU B 455 REMARK 465 GLY B 456 REMARK 465 GLY B 457 REMARK 465 ILE B 458 REMARK 465 TRP B 459 REMARK 465 GLU B 460 REMARK 465 ASP B 461 REMARK 465 GLU B 462 REMARK 465 ASP B 463 REMARK 465 ALA B 464 REMARK 465 ARG B 465 REMARK 465 ASN B 466 REMARK 465 PHE B 467 REMARK 465 TYR B 468 REMARK 465 GLU B 469 REMARK 465 ASN B 470 REMARK 465 LEU B 471 REMARK 465 ILE B 472 REMARK 465 ASP B 473 REMARK 465 LEU B 474 REMARK 465 LYS B 475 REMARK 465 ALA B 476 REMARK 465 PHE B 477 REMARK 465 VAL B 478 REMARK 465 PRO B 479 REMARK 465 ALA B 480 REMARK 465 ILE B 481 REMARK 465 LEU B 482 REMARK 465 PHE B 483 REMARK 465 LYS B 484 REMARK 465 ASP B 485 REMARK 465 ASN B 486 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 HIS A 371 CB - CG - ND1 ANGL. DEV. = 9.6 DEGREES REMARK 500 HIS B 366 CB - CG - ND1 ANGL. DEV. = 9.3 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 158 -59.06 -25.44 REMARK 500 THR A 256 95.67 65.55 REMARK 500 ASP A 298 79.14 -112.04 REMARK 500 GLU A 300 -64.18 -106.73 REMARK 500 ILE A 343 -64.93 -101.55 REMARK 500 GLU A 390 -101.54 54.60 REMARK 500 LEU A 391 88.66 55.89 REMARK 500 GLU A 393 -126.59 -86.60 REMARK 500 SER B 154 21.00 -150.66 REMARK 500 GLU B 300 -63.82 -103.30 REMARK 500 GLU B 390 -163.02 63.31 REMARK 500 LEU B 391 110.07 67.09 REMARK 500 SER B 392 53.88 -148.76 REMARK 500 GLU B 393 -104.21 -67.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CEK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SECOND MIF4G DOMAIN OF HUMAN REMARK 900 NONSENSE MEDIATED DECAY FACTOR UPF2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 N-TERMINAL GAMG LEFT AFTER HIS-TAG CLEAVAGE DBREF 4CEM A 121 486 UNP Q9HAU5 RENT2_HUMAN 121 486 DBREF 4CEM B 121 486 UNP Q9HAU5 RENT2_HUMAN 121 486 SEQADV 4CEM GLY A 117 UNP Q9HAU5 EXPRESSION TAG SEQADV 4CEM ALA A 118 UNP Q9HAU5 EXPRESSION TAG SEQADV 4CEM MSE A 119 UNP Q9HAU5 EXPRESSION TAG SEQADV 4CEM GLY A 120 UNP Q9HAU5 EXPRESSION TAG SEQADV 4CEM ILE A 168 UNP Q9HAU5 LEU 168 CONFLICT SEQADV 4CEM GLY B 117 UNP Q9HAU5 EXPRESSION TAG SEQADV 4CEM ALA B 118 UNP Q9HAU5 EXPRESSION TAG SEQADV 4CEM MSE B 119 UNP Q9HAU5 EXPRESSION TAG SEQADV 4CEM GLY B 120 UNP Q9HAU5 EXPRESSION TAG SEQADV 4CEM ILE B 168 UNP Q9HAU5 LEU 168 CONFLICT SEQRES 1 A 370 GLY ALA MSE GLY MSE LYS GLU LYS GLU GLU SER ILE GLN SEQRES 2 A 370 LEU HIS GLN GLU ALA TRP GLU ARG HIS HIS LEU ARG LYS SEQRES 3 A 370 GLU LEU ARG SER LYS ASN GLN ASN ALA PRO ASP SER ARG SEQRES 4 A 370 PRO GLU GLU ASN PHE PHE SER ARG LEU ASP SER SER ILE SEQRES 5 A 370 LYS LYS ASN THR ALA PHE VAL LYS LYS LEU LYS THR ILE SEQRES 6 A 370 THR GLU GLN GLN ARG ASP SER LEU SER HIS ASP PHE ASN SEQRES 7 A 370 GLY LEU ASN LEU SER LYS TYR ILE ALA GLU ALA VAL ALA SEQRES 8 A 370 SER ILE VAL GLU ALA LYS LEU LYS ILE SER ASP VAL ASN SEQRES 9 A 370 CYS ALA VAL HIS LEU CYS SER LEU PHE HIS GLN ARG TYR SEQRES 10 A 370 ALA ASP PHE ALA PRO SER LEU LEU GLN VAL TRP LYS LYS SEQRES 11 A 370 HIS PHE GLU ALA ARG LYS GLU GLU LYS THR PRO ASN ILE SEQRES 12 A 370 THR LYS LEU ARG THR ASP LEU ARG PHE ILE ALA GLU LEU SEQRES 13 A 370 THR ILE VAL GLY ILE PHE THR ASP LYS GLU GLY LEU SER SEQRES 14 A 370 LEU ILE TYR GLU GLN LEU LYS ASN ILE ILE ASN ALA ASP SEQRES 15 A 370 ARG GLU SER HIS THR HIS VAL SER VAL VAL ILE SER PHE SEQRES 16 A 370 CYS ARG HIS CYS GLY ASP ASP ILE ALA GLY LEU VAL PRO SEQRES 17 A 370 ARG LYS VAL LYS SER ALA ALA GLU LYS PHE ASN LEU SER SEQRES 18 A 370 PHE PRO PRO SER GLU ILE ILE SER PRO GLU LYS GLN GLN SEQRES 19 A 370 PRO PHE GLN ASN LEU LEU LYS GLU TYR PHE THR SER LEU SEQRES 20 A 370 THR LYS HIS LEU LYS ARG ASP HIS ARG GLU LEU GLN ASN SEQRES 21 A 370 THR GLU ARG GLN ASN ARG ARG ILE LEU HIS SER LYS GLY SEQRES 22 A 370 GLU LEU SER GLU ASP ARG HIS LYS GLN TYR GLU GLU PHE SEQRES 23 A 370 ALA MSE SER TYR GLN LYS LEU LEU ALA ASN SER GLN SER SEQRES 24 A 370 LEU ALA ASP LEU LEU ASP GLU ASN MSE PRO ASP LEU PRO SEQRES 25 A 370 GLN ASP LYS PRO THR PRO GLU GLU HIS GLY PRO GLY ILE SEQRES 26 A 370 ASP ILE PHE THR PRO GLY LYS PRO GLY GLU TYR ASP LEU SEQRES 27 A 370 GLU GLY GLY ILE TRP GLU ASP GLU ASP ALA ARG ASN PHE SEQRES 28 A 370 TYR GLU ASN LEU ILE ASP LEU LYS ALA PHE VAL PRO ALA SEQRES 29 A 370 ILE LEU PHE LYS ASP ASN SEQRES 1 B 370 GLY ALA MSE GLY MSE LYS GLU LYS GLU GLU SER ILE GLN SEQRES 2 B 370 LEU HIS GLN GLU ALA TRP GLU ARG HIS HIS LEU ARG LYS SEQRES 3 B 370 GLU LEU ARG SER LYS ASN GLN ASN ALA PRO ASP SER ARG SEQRES 4 B 370 PRO GLU GLU ASN PHE PHE SER ARG LEU ASP SER SER ILE SEQRES 5 B 370 LYS LYS ASN THR ALA PHE VAL LYS LYS LEU LYS THR ILE SEQRES 6 B 370 THR GLU GLN GLN ARG ASP SER LEU SER HIS ASP PHE ASN SEQRES 7 B 370 GLY LEU ASN LEU SER LYS TYR ILE ALA GLU ALA VAL ALA SEQRES 8 B 370 SER ILE VAL GLU ALA LYS LEU LYS ILE SER ASP VAL ASN SEQRES 9 B 370 CYS ALA VAL HIS LEU CYS SER LEU PHE HIS GLN ARG TYR SEQRES 10 B 370 ALA ASP PHE ALA PRO SER LEU LEU GLN VAL TRP LYS LYS SEQRES 11 B 370 HIS PHE GLU ALA ARG LYS GLU GLU LYS THR PRO ASN ILE SEQRES 12 B 370 THR LYS LEU ARG THR ASP LEU ARG PHE ILE ALA GLU LEU SEQRES 13 B 370 THR ILE VAL GLY ILE PHE THR ASP LYS GLU GLY LEU SER SEQRES 14 B 370 LEU ILE TYR GLU GLN LEU LYS ASN ILE ILE ASN ALA ASP SEQRES 15 B 370 ARG GLU SER HIS THR HIS VAL SER VAL VAL ILE SER PHE SEQRES 16 B 370 CYS ARG HIS CYS GLY ASP ASP ILE ALA GLY LEU VAL PRO SEQRES 17 B 370 ARG LYS VAL LYS SER ALA ALA GLU LYS PHE ASN LEU SER SEQRES 18 B 370 PHE PRO PRO SER GLU ILE ILE SER PRO GLU LYS GLN GLN SEQRES 19 B 370 PRO PHE GLN ASN LEU LEU LYS GLU TYR PHE THR SER LEU SEQRES 20 B 370 THR LYS HIS LEU LYS ARG ASP HIS ARG GLU LEU GLN ASN SEQRES 21 B 370 THR GLU ARG GLN ASN ARG ARG ILE LEU HIS SER LYS GLY SEQRES 22 B 370 GLU LEU SER GLU ASP ARG HIS LYS GLN TYR GLU GLU PHE SEQRES 23 B 370 ALA MSE SER TYR GLN LYS LEU LEU ALA ASN SER GLN SER SEQRES 24 B 370 LEU ALA ASP LEU LEU ASP GLU ASN MSE PRO ASP LEU PRO SEQRES 25 B 370 GLN ASP LYS PRO THR PRO GLU GLU HIS GLY PRO GLY ILE SEQRES 26 B 370 ASP ILE PHE THR PRO GLY LYS PRO GLY GLU TYR ASP LEU SEQRES 27 B 370 GLU GLY GLY ILE TRP GLU ASP GLU ASP ALA ARG ASN PHE SEQRES 28 B 370 TYR GLU ASN LEU ILE ASP LEU LYS ALA PHE VAL PRO ALA SEQRES 29 B 370 ILE LEU PHE LYS ASP ASN MODRES 4CEM MSE A 121 MET SELENOMETHIONINE MODRES 4CEM MSE A 404 MET SELENOMETHIONINE MODRES 4CEM MSE A 424 MET SELENOMETHIONINE MODRES 4CEM MSE B 121 MET SELENOMETHIONINE MODRES 4CEM MSE B 404 MET SELENOMETHIONINE MODRES 4CEM MSE B 424 MET SELENOMETHIONINE HET MSE A 121 8 HET MSE A 404 8 HET MSE A 424 8 HET MSE B 121 8 HET MSE B 404 8 HET MSE B 424 8 HETNAM MSE SELENOMETHIONINE FORMUL 2 MSE 6(C5 H11 N O2 SE) FORMUL 3 HOH *54(H2 O) HELIX 1 1 MSE A 121 ASN A 150 1 30 HELIX 2 2 ALA A 151 ARG A 155 5 5 HELIX 3 3 GLU A 157 ARG A 163 1 7 HELIX 4 4 SER A 167 LEU A 178 1 12 HELIX 5 5 LYS A 179 ILE A 181 5 3 HELIX 6 6 THR A 182 GLN A 184 5 3 HELIX 7 7 GLN A 185 LEU A 196 1 12 HELIX 8 8 TYR A 201 ALA A 212 1 12 HELIX 9 9 LYS A 215 SER A 217 5 3 HELIX 10 10 ASP A 218 TYR A 233 1 16 HELIX 11 11 ASP A 235 GLU A 254 1 20 HELIX 12 12 ASN A 258 VAL A 275 1 18 HELIX 13 13 THR A 279 ASP A 298 1 20 HELIX 14 14 HIS A 304 GLY A 321 1 18 HELIX 15 15 PRO A 324 ASN A 335 1 12 HELIX 16 16 SER A 345 ASN A 376 1 32 HELIX 17 17 ARG A 382 SER A 387 1 6 HELIX 18 18 GLN A 398 LEU A 420 1 23 HELIX 19 19 MSE B 121 ASN B 150 1 30 HELIX 20 20 ALA B 151 ARG B 155 5 5 HELIX 21 21 GLU B 157 SER B 162 1 6 HELIX 22 22 SER B 167 LEU B 178 1 12 HELIX 23 23 LYS B 179 ILE B 181 5 3 HELIX 24 24 THR B 182 GLN B 184 5 3 HELIX 25 25 GLN B 185 LEU B 196 1 12 HELIX 26 26 TYR B 201 ALA B 212 1 12 HELIX 27 27 LYS B 215 SER B 217 5 3 HELIX 28 28 ASP B 218 TYR B 233 1 16 HELIX 29 29 ASP B 235 GLU B 253 1 19 HELIX 30 30 ASN B 258 VAL B 275 1 18 HELIX 31 31 THR B 279 ASP B 298 1 20 HELIX 32 32 HIS B 304 ALA B 320 1 17 HELIX 33 33 PRO B 324 ASN B 335 1 12 HELIX 34 34 SER B 345 ILE B 384 1 40 HELIX 35 35 ASP B 394 LEU B 420 1 27 LINK C MSE A 121 N LYS A 122 1555 1555 1.33 LINK C ALA A 403 N MSE A 404 1555 1555 1.33 LINK C MSE A 404 N SER A 405 1555 1555 1.33 LINK C ASN A 423 N MSE A 424 1555 1555 1.33 LINK C MSE A 424 N PRO A 425 1555 1555 1.35 LINK C MSE B 121 N LYS B 122 1555 1555 1.33 LINK C ALA B 403 N MSE B 404 1555 1555 1.33 LINK C MSE B 404 N SER B 405 1555 1555 1.33 LINK C ASN B 423 N MSE B 424 1555 1555 1.33 LINK C MSE B 424 N PRO B 425 1555 1555 1.35 CRYST1 101.080 101.080 158.880 90.00 90.00 120.00 P 65 12 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 0.009893 0.005712 0.000000 0.00000 SCALE2 0.000000 0.011424 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006294 0.00000 HETATM 1 N MSE A 121 16.446 3.574 39.492 1.00 95.16 N HETATM 2 CA MSE A 121 16.663 4.367 40.739 1.00 98.55 C HETATM 3 C MSE A 121 16.191 5.788 40.542 1.00 90.55 C HETATM 4 O MSE A 121 16.354 6.368 39.466 1.00 84.62 O HETATM 5 CB MSE A 121 18.150 4.301 41.111 1.00109.17 C HETATM 6 CG MSE A 121 18.502 4.947 42.454 1.00117.55 C HETATM 7 SE MSE A 121 17.416 4.251 43.955 1.00141.51 SE HETATM 8 CE MSE A 121 17.369 2.333 43.485 1.00126.10 C