HEADER RNA BINDING PROTEIN/RNA 16-JUN-21 7F3J TITLE CRYSTAL STRUCTURE OF HUMAN YBX2 CSD IN COMPLEX WITH M5C RNA IN SPACE TITLE 2 GROUP P1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: Y-BOX-BINDING PROTEIN 2; COMPND 3 CHAIN: A, C, E, G; COMPND 4 SYNONYM: CONTRIN,DNA-BINDING PROTEIN C,DBPC,GERM CELL-SPECIFIC Y-BOX- COMPND 5 BINDING PROTEIN,MSY2 HOMOLOG; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(*UP*CP*AP*UP*(5MC))-3'); COMPND 10 CHAIN: B, D, F, H; COMPND 11 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: YBX2, CSDA3, MSY2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS COMPLEX, PROTEIN-RNA, YBX, COLD-SHOCK DOMAIN, RNA BINDING PROTEIN, KEYWDS 2 RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHANG,Y.HUANG REVDAT 2 29-NOV-23 7F3J 1 REMARK REVDAT 1 22-JUN-22 7F3J 0 JRNL AUTH Y.ZHANG,Y.HUANG JRNL TITL CRYSTAL STRUCTURE OF HUMAN YBX2 CSD IN COMPLEX WITH M5C RNA JRNL TITL 2 IN SPACE GROUP P1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.560 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 27986 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1967 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.7400 - 4.6900 0.99 1969 143 0.1867 0.1962 REMARK 3 2 4.6900 - 3.7300 0.99 1966 147 0.1502 0.1700 REMARK 3 3 3.7300 - 3.2600 0.99 1975 150 0.1710 0.2127 REMARK 3 4 3.2600 - 2.9600 0.99 1966 144 0.1907 0.2596 REMARK 3 5 2.9600 - 2.7500 0.98 1941 151 0.2129 0.2558 REMARK 3 6 2.7500 - 2.5900 0.98 1978 142 0.2147 0.2677 REMARK 3 7 2.5900 - 2.4600 0.98 1944 144 0.2140 0.2917 REMARK 3 8 2.4600 - 2.3500 0.97 1932 149 0.1912 0.2462 REMARK 3 9 2.3500 - 2.2600 0.97 1928 137 0.1947 0.2467 REMARK 3 10 2.2600 - 2.1800 0.97 1948 156 0.1892 0.2248 REMARK 3 11 2.1800 - 2.1100 0.94 1847 134 0.1885 0.2505 REMARK 3 12 2.1100 - 2.0500 0.86 1712 135 0.1982 0.2306 REMARK 3 13 2.0500 - 2.0000 0.77 1496 117 0.2096 0.2400 REMARK 3 14 2.0000 - 1.9500 0.71 1417 118 0.2147 0.2793 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.211 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.251 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.59 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 3276 REMARK 3 ANGLE : 1.102 4510 REMARK 3 CHIRALITY : 0.063 506 REMARK 3 PLANARITY : 0.007 534 REMARK 3 DIHEDRAL : 22.092 594 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 2 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: chain "A" REMARK 3 SELECTION : chain "C" REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: chain "A" REMARK 3 SELECTION : (chain "E" and resid 89 through 177) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 3 REMARK 3 REFERENCE SELECTION: chain "A" REMARK 3 SELECTION : (chain "G" and resid 89 through 177) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: chain "B" REMARK 3 SELECTION : chain "D" REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: chain "B" REMARK 3 SELECTION : chain "F" REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 3 REMARK 3 REFERENCE SELECTION: chain "B" REMARK 3 SELECTION : chain "H" REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7F3J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022773. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : 0.97915 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29797 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27600 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 REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6A6J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG 4000, 0.1 M TRIS-HCL, PH REMARK 280 8.5, 0.2 M LITHIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H 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 ALA A 85 REMARK 465 ASP A 86 REMARK 465 LYS A 87 REMARK 465 PRO A 88 REMARK 465 U B 6 REMARK 465 U B 7 REMARK 465 ALA C 85 REMARK 465 ASP C 86 REMARK 465 LYS C 87 REMARK 465 PRO C 88 REMARK 465 U D 6 REMARK 465 U D 7 REMARK 465 ALA E 85 REMARK 465 ASP E 86 REMARK 465 LYS E 87 REMARK 465 U F 6 REMARK 465 U F 7 REMARK 465 ALA G 85 REMARK 465 ASP G 86 REMARK 465 LYS G 87 REMARK 465 U H 6 REMARK 465 U H 7 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PHE E 101 N4 5MC F 5 1.33 REMARK 500 O HOH A 212 O HOH A 257 1.90 REMARK 500 O HOH A 234 O HOH A 283 1.93 REMARK 500 O HOH E 257 O HOH E 262 1.94 REMARK 500 OE1 GLN G 123 O HOH G 201 1.95 REMARK 500 O HOH E 247 O HOH E 259 1.95 REMARK 500 O HOH A 244 O HOH A 279 2.09 REMARK 500 O HOH C 272 O HOH C 294 2.10 REMARK 500 O HOH C 271 O HOH C 274 2.18 REMARK 500 N VAL C 89 O HOH C 201 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH E 257 O HOH G 230 1655 1.99 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 LEU A 135 163.60 61.93 REMARK 500 LEU C 135 164.16 65.65 REMARK 500 GLU C 152 -92.73 24.85 REMARK 500 LYS C 153 54.83 -116.00 REMARK 500 GLU E 152 -59.30 2.90 REMARK 500 LYS E 153 51.56 -116.35 REMARK 500 LYS G 153 55.47 -111.47 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 C 151 GLU C 152 134.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6A6J RELATED DB: PDB REMARK 900 ZFYBX1 COMPLEXED WITH M5C RNA REMARK 900 RELATED ID: 6A6L RELATED DB: PDB REMARK 900 HYBX1 COMPLEXED WITH M5C RNA REMARK 900 RELATED ID: 5YTX RELATED DB: PDB REMARK 900 HYBX1 COMPLEXED WITH RNA REMARK 900 RELATED ID: 5YTS RELATED DB: PDB REMARK 900 HYBX1 COMPLEXED WITH RNA REMARK 900 RELATED ID: 5YTT RELATED DB: PDB REMARK 900 HYBX1 COMPLEXED WITH RNA REMARK 900 RELATED ID: 5YTV RELATED DB: PDB REMARK 900 HYBX1 COMPLEXED WITH RNA DBREF 7F3J A 85 177 UNP Q9Y2T7 YBOX2_HUMAN 85 177 DBREF 7F3J B 1 7 PDB 7F3J 7F3J 1 7 DBREF 7F3J C 85 177 UNP Q9Y2T7 YBOX2_HUMAN 85 177 DBREF 7F3J D 1 7 PDB 7F3J 7F3J 1 7 DBREF 7F3J E 85 177 UNP Q9Y2T7 YBOX2_HUMAN 85 177 DBREF 7F3J F 1 7 PDB 7F3J 7F3J 1 7 DBREF 7F3J G 85 177 UNP Q9Y2T7 YBOX2_HUMAN 85 177 DBREF 7F3J H 1 7 PDB 7F3J 7F3J 1 7 SEQADV 7F3J THR A 92 UNP Q9Y2T7 ILE 92 ENGINEERED MUTATION SEQADV 7F3J LYS A 93 UNP Q9Y2T7 GLN 93 ENGINEERED MUTATION SEQADV 7F3J THR C 92 UNP Q9Y2T7 ILE 92 ENGINEERED MUTATION SEQADV 7F3J LYS C 93 UNP Q9Y2T7 GLN 93 ENGINEERED MUTATION SEQADV 7F3J THR E 92 UNP Q9Y2T7 ILE 92 ENGINEERED MUTATION SEQADV 7F3J LYS E 93 UNP Q9Y2T7 GLN 93 ENGINEERED MUTATION SEQADV 7F3J THR G 92 UNP Q9Y2T7 ILE 92 ENGINEERED MUTATION SEQADV 7F3J LYS G 93 UNP Q9Y2T7 GLN 93 ENGINEERED MUTATION SEQRES 1 A 93 ALA ASP LYS PRO VAL LEU ALA THR LYS VAL LEU GLY THR SEQRES 2 A 93 VAL LYS TRP PHE ASN VAL ARG ASN GLY TYR GLY PHE ILE SEQRES 3 A 93 ASN ARG ASN ASP THR LYS GLU ASP VAL PHE VAL HIS GLN SEQRES 4 A 93 THR ALA ILE LYS ARG ASN ASN PRO ARG LYS PHE LEU ARG SEQRES 5 A 93 SER VAL GLY ASP GLY GLU THR VAL GLU PHE ASP VAL VAL SEQRES 6 A 93 GLU GLY GLU LYS GLY ALA GLU ALA THR ASN VAL THR GLY SEQRES 7 A 93 PRO GLY GLY VAL PRO VAL LYS GLY SER ARG TYR ALA PRO SEQRES 8 A 93 ASN ARG SEQRES 1 B 7 U C A U 5MC U U SEQRES 1 C 93 ALA ASP LYS PRO VAL LEU ALA THR LYS VAL LEU GLY THR SEQRES 2 C 93 VAL LYS TRP PHE ASN VAL ARG ASN GLY TYR GLY PHE ILE SEQRES 3 C 93 ASN ARG ASN ASP THR LYS GLU ASP VAL PHE VAL HIS GLN SEQRES 4 C 93 THR ALA ILE LYS ARG ASN ASN PRO ARG LYS PHE LEU ARG SEQRES 5 C 93 SER VAL GLY ASP GLY GLU THR VAL GLU PHE ASP VAL VAL SEQRES 6 C 93 GLU GLY GLU LYS GLY ALA GLU ALA THR ASN VAL THR GLY SEQRES 7 C 93 PRO GLY GLY VAL PRO VAL LYS GLY SER ARG TYR ALA PRO SEQRES 8 C 93 ASN ARG SEQRES 1 D 7 U C A U 5MC U U SEQRES 1 E 93 ALA ASP LYS PRO VAL LEU ALA THR LYS VAL LEU GLY THR SEQRES 2 E 93 VAL LYS TRP PHE ASN VAL ARG ASN GLY TYR GLY PHE ILE SEQRES 3 E 93 ASN ARG ASN ASP THR LYS GLU ASP VAL PHE VAL HIS GLN SEQRES 4 E 93 THR ALA ILE LYS ARG ASN ASN PRO ARG LYS PHE LEU ARG SEQRES 5 E 93 SER VAL GLY ASP GLY GLU THR VAL GLU PHE ASP VAL VAL SEQRES 6 E 93 GLU GLY GLU LYS GLY ALA GLU ALA THR ASN VAL THR GLY SEQRES 7 E 93 PRO GLY GLY VAL PRO VAL LYS GLY SER ARG TYR ALA PRO SEQRES 8 E 93 ASN ARG SEQRES 1 F 7 U C A U 5MC U U SEQRES 1 G 93 ALA ASP LYS PRO VAL LEU ALA THR LYS VAL LEU GLY THR SEQRES 2 G 93 VAL LYS TRP PHE ASN VAL ARG ASN GLY TYR GLY PHE ILE SEQRES 3 G 93 ASN ARG ASN ASP THR LYS GLU ASP VAL PHE VAL HIS GLN SEQRES 4 G 93 THR ALA ILE LYS ARG ASN ASN PRO ARG LYS PHE LEU ARG SEQRES 5 G 93 SER VAL GLY ASP GLY GLU THR VAL GLU PHE ASP VAL VAL SEQRES 6 G 93 GLU GLY GLU LYS GLY ALA GLU ALA THR ASN VAL THR GLY SEQRES 7 G 93 PRO GLY GLY VAL PRO VAL LYS GLY SER ARG TYR ALA PRO SEQRES 8 G 93 ASN ARG SEQRES 1 H 7 U C A U 5MC U U HET 5MC B 5 21 HET 5MC D 5 21 HET 5MC F 5 21 HET 5MC H 5 21 HETNAM 5MC 5-METHYLCYTIDINE-5'-MONOPHOSPHATE FORMUL 2 5MC 4(C10 H16 N3 O8 P) FORMUL 9 HOH *348(H2 O) HELIX 1 AA1 THR A 124 ILE A 126 5 3 HELIX 2 AA2 GLY A 162 VAL A 166 5 5 HELIX 3 AA3 THR C 124 ILE C 126 5 3 HELIX 4 AA4 GLY C 162 VAL C 166 5 5 HELIX 5 AA5 THR E 124 ILE E 126 5 3 HELIX 6 AA6 GLY E 162 VAL E 166 5 5 HELIX 7 AA7 THR G 124 ILE G 126 5 3 HELIX 8 AA8 GLY G 162 VAL G 166 5 5 SHEET 1 AA1 6 ALA A 91 ASN A 102 0 SHEET 2 AA1 6 TYR A 107 ARG A 112 -1 O ASN A 111 N THR A 97 SHEET 3 AA1 6 ASP A 118 HIS A 122 -1 O VAL A 119 N ILE A 110 SHEET 4 AA1 6 GLY A 154 THR A 161 1 O ALA A 157 N PHE A 120 SHEET 5 AA1 6 THR A 143 GLY A 151 -1 N VAL A 149 O GLU A 156 SHEET 6 AA1 6 ALA A 91 ASN A 102 -1 N VAL A 94 O PHE A 146 SHEET 1 AA2 6 ALA C 91 ASN C 102 0 SHEET 2 AA2 6 TYR C 107 ARG C 112 -1 O TYR C 107 N ASN C 102 SHEET 3 AA2 6 ASP C 118 HIS C 122 -1 O VAL C 119 N ILE C 110 SHEET 4 AA2 6 GLY C 154 THR C 161 1 O ALA C 157 N PHE C 120 SHEET 5 AA2 6 THR C 143 GLY C 151 -1 N ASP C 147 O THR C 158 SHEET 6 AA2 6 ALA C 91 ASN C 102 -1 N VAL C 94 O PHE C 146 SHEET 1 AA3 6 VAL E 89 ASN E 102 0 SHEET 2 AA3 6 TYR E 107 ARG E 112 -1 O ASN E 111 N THR E 97 SHEET 3 AA3 6 ASP E 118 HIS E 122 -1 O VAL E 119 N ILE E 110 SHEET 4 AA3 6 GLY E 154 THR E 161 1 O ALA E 157 N PHE E 120 SHEET 5 AA3 6 THR E 143 GLY E 151 -1 N GLU E 145 O THR E 161 SHEET 6 AA3 6 VAL E 89 ASN E 102 -1 N VAL E 94 O PHE E 146 SHEET 1 AA4 6 VAL G 89 ASN G 102 0 SHEET 2 AA4 6 TYR G 107 ARG G 112 -1 O TYR G 107 N ASN G 102 SHEET 3 AA4 6 ASP G 118 HIS G 122 -1 O VAL G 119 N ILE G 110 SHEET 4 AA4 6 GLY G 154 THR G 161 1 O ALA G 157 N PHE G 120 SHEET 5 AA4 6 THR G 143 GLY G 151 -1 N GLU G 145 O THR G 161 SHEET 6 AA4 6 VAL G 89 ASN G 102 -1 N VAL G 94 O PHE G 146 LINK O3' U B 4 P 5MC B 5 1555 1555 1.61 LINK O3' U D 4 P 5MC D 5 1555 1555 1.60 LINK O3' U F 4 P 5MC F 5 1555 1555 1.61 LINK O3' U H 4 P 5MC H 5 1555 1555 1.60 CRYST1 42.616 46.364 57.704 69.26 85.60 90.02 P 1 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 0.023465 0.000006 -0.001933 0.00000 SCALE2 0.000000 0.021568 -0.008194 0.00000 SCALE3 0.000000 0.000000 0.018593 0.00000 MTRIX1 1 0.999996 0.001522 0.002423 21.32777 1 MTRIX2 1 0.001520 -0.999999 0.000565 12.53163 1 MTRIX3 1 0.002424 -0.000561 -0.999997 -40.97963 1 MTRIX1 2 -0.995560 -0.055847 0.075772 58.80698 1 MTRIX2 2 -0.089884 0.803034 -0.589116 13.02085 1 MTRIX3 2 -0.027947 -0.593311 -0.804488 -32.76751 1 MTRIX1 3 -0.996431 -0.041895 0.073277 37.38571 1 MTRIX2 3 0.077369 -0.800400 0.594453 46.10903 1 MTRIX3 3 0.033746 0.598001 0.800785 -8.66310 1 MTRIX1 4 0.999967 0.004887 -0.006438 21.22340 1 MTRIX2 4 0.005005 -0.999818 0.018383 12.63252 1 MTRIX3 4 -0.006347 -0.018415 -0.999810 -40.56737 1 MTRIX1 5 -0.993713 -0.087835 0.069420 59.20490 1 MTRIX2 5 -0.111948 0.772252 -0.625375 13.87916 1 MTRIX3 5 0.001320 -0.629215 -0.777230 -32.69620 1 MTRIX1 6 -0.996130 -0.047244 0.074117 37.50456 1 MTRIX2 6 0.083838 -0.763917 0.639846 45.75969 1 MTRIX3 6 0.026391 0.643583 0.764921 -9.55521 1