HEADER RNA BINDING PROTEIN 15-AUG-14 4R3H TITLE THE CRYSTAL STRUCTURE OF AN APO RNA BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTH DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PUTATIVE SPLICING FACTOR YT521, YT521-B; COMPND 5 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: YTHDC1, KIAA1966, YT521; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL KEYWDS STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, RNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.XU,K.LIU,W.TEMPEL,Y.LI,C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS,J.MIN, AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 28-FEB-24 4R3H 1 REMARK SEQADV REVDAT 3 19-NOV-14 4R3H 1 JRNL REVDAT 2 01-OCT-14 4R3H 1 JRNL REVDAT 1 17-SEP-14 4R3H 0 JRNL AUTH C.XU,X.WANG,K.LIU,I.A.ROUNDTREE,W.TEMPEL,Y.LI,Z.LU,C.HE, JRNL AUTH 2 J.MIN JRNL TITL STRUCTURAL BASIS FOR SELECTIVE BINDING OF M(6)A RNA BY THE JRNL TITL 2 YTHDC1 YTH DOMAIN. JRNL REF NAT.CHEM.BIOL. V. 10 927 2014 JRNL REFN ISSN 1552-4450 JRNL PMID 25242552 JRNL DOI 10.1038/NCHEMBIO.1654 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 24951 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS (SFTOOLS) REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1007 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1787 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE SET COUNT : 26 REMARK 3 BIN FREE R VALUE : 0.4610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2427 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.80000 REMARK 3 B22 (A**2) : -1.01000 REMARK 3 B33 (A**2) : -0.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.86000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.794 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2499 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2400 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3381 ; 1.338 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5513 ; 0.761 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 310 ; 6.242 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;30.688 ;23.529 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 428 ;12.366 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;16.973 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 377 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2782 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 587 ; 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): 1246 ; 1.634 ; 1.981 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1245 ; 1.633 ; 1.979 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1551 ; 2.446 ; 2.953 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): 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 344 A 507 REMARK 3 ORIGIN FOR THE GROUP (A): 21.5695 22.7512 1.3514 REMARK 3 T TENSOR REMARK 3 T11: 0.0425 T22: 0.0164 REMARK 3 T33: 0.0426 T12: -0.0059 REMARK 3 T13: -0.0130 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 2.3007 L22: 3.6135 REMARK 3 L33: 2.1113 L12: 0.7808 REMARK 3 L13: -0.2183 L23: -0.2657 REMARK 3 S TENSOR REMARK 3 S11: 0.0352 S12: 0.1464 S13: -0.1608 REMARK 3 S21: -0.1413 S22: 0.0156 S23: 0.0720 REMARK 3 S31: 0.0810 S32: -0.0058 S33: -0.0508 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 344 B 507 REMARK 3 ORIGIN FOR THE GROUP (A): 25.5053 49.3072 26.4192 REMARK 3 T TENSOR REMARK 3 T11: 0.0073 T22: 0.0077 REMARK 3 T33: 0.0187 T12: -0.0034 REMARK 3 T13: 0.0067 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 2.5880 L22: 4.0764 REMARK 3 L33: 2.5060 L12: 0.2997 REMARK 3 L13: 0.2142 L23: 1.1080 REMARK 3 S TENSOR REMARK 3 S11: 0.0011 S12: 0.0444 S13: -0.0923 REMARK 3 S21: -0.0919 S22: 0.0895 S23: -0.2525 REMARK 3 S31: 0.0326 S32: 0.0958 S33: -0.0906 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: STRUCTURE OF AN ISOMORPHOUS CRYSTAL WAS REMARK 3 SOLVED BY MOLECULAR REPLACEMENT USING PHASER AND COORDINATES REMARK 3 FROM PDB ENTRY 2YUD. PHASE IMPROVEMENT AND AUTOMATED MODEL REMARK 3 BUILDING WERE PERFORMED WITH ARP/WARP. COOT WAS USED FOR REMARK 3 INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH REMARK 3 MOLPROBITY. REMARK 4 REMARK 4 4R3H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086851. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28931 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 27.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.90100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2M AMMONIUM SULPHATE, REMARK 280 0.1M BIS-TRIS, PH 6.5, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 51.51300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 PRO A 431 REMARK 465 ALA A 432 REMARK 465 GLY A 433 REMARK 465 MET A 434 REMARK 465 SER A 435 REMARK 465 ALA A 436 REMARK 465 LYS A 437 REMARK 465 ARG A 508 REMARK 465 HIS A 509 REMARK 465 PRO B 431 REMARK 465 ALA B 432 REMARK 465 GLY B 433 REMARK 465 MET B 434 REMARK 465 SER B 435 REMARK 465 ALA B 436 REMARK 465 LYS B 437 REMARK 465 MET B 438 REMARK 465 LEU B 439 REMARK 465 ARG B 508 REMARK 465 HIS B 509 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 366 CG CD OE1 OE2 REMARK 470 LYS A 374 CD CE NZ REMARK 470 ARG A 395 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 405 OE1 OE2 REMARK 470 SER A 424 OG REMARK 470 LEU A 430 CD1 CD2 REMARK 470 MET A 438 CG SD CE REMARK 470 LYS A 444 CE NZ REMARK 470 LYS A 457 CE NZ REMARK 470 ARG A 475 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 483 CD OE1 OE2 REMARK 470 HIS A 505 CG ND1 CD2 CE1 NE2 REMARK 470 ASP B 354 CG OD1 OD2 REMARK 470 ASN B 363 CG OD1 ND2 REMARK 470 LYS B 374 CE NZ REMARK 470 LYS B 385 CG CD CE NZ REMARK 470 HIS B 420 CG ND1 CD2 CE1 NE2 REMARK 470 SER B 424 OG REMARK 470 HIS B 427 CG ND1 CD2 CE1 NE2 REMARK 470 LEU B 430 CD1 CD2 REMARK 470 LYS B 444 CG CD CE NZ REMARK 470 ARG B 475 NE CZ NH1 NH2 REMARK 470 HIS B 505 CG ND1 CD2 CE1 NE2 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 405 -1.62 70.10 REMARK 500 LYS A 506 -79.62 -77.29 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 SO4 B 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4R3I RELATED DB: PDB DBREF 4R3H A 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 DBREF 4R3H B 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 SEQADV 4R3H GLY A 344 UNP Q96MU7 EXPRESSION TAG SEQADV 4R3H GLY B 344 UNP Q96MU7 EXPRESSION TAG SEQRES 1 A 166 GLY THR SER LYS LEU LYS TYR VAL LEU GLN ASP ALA ARG SEQRES 2 A 166 PHE PHE LEU ILE LYS SER ASN ASN HIS GLU ASN VAL SER SEQRES 3 A 166 LEU ALA LYS ALA LYS GLY VAL TRP SER THR LEU PRO VAL SEQRES 4 A 166 ASN GLU LYS LYS LEU ASN LEU ALA PHE ARG SER ALA ARG SEQRES 5 A 166 SER VAL ILE LEU ILE PHE SER VAL ARG GLU SER GLY LYS SEQRES 6 A 166 PHE GLN GLY PHE ALA ARG LEU SER SER GLU SER HIS HIS SEQRES 7 A 166 GLY GLY SER PRO ILE HIS TRP VAL LEU PRO ALA GLY MET SEQRES 8 A 166 SER ALA LYS MET LEU GLY GLY VAL PHE LYS ILE ASP TRP SEQRES 9 A 166 ILE CYS ARG ARG GLU LEU PRO PHE THR LYS SER ALA HIS SEQRES 10 A 166 LEU THR ASN PRO TRP ASN GLU HIS LYS PRO VAL LYS ILE SEQRES 11 A 166 GLY ARG ASP GLY GLN GLU ILE GLU LEU GLU CYS GLY THR SEQRES 12 A 166 GLN LEU CYS LEU LEU PHE PRO PRO ASP GLU SER ILE ASP SEQRES 13 A 166 LEU TYR GLN VAL ILE HIS LYS MET ARG HIS SEQRES 1 B 166 GLY THR SER LYS LEU LYS TYR VAL LEU GLN ASP ALA ARG SEQRES 2 B 166 PHE PHE LEU ILE LYS SER ASN ASN HIS GLU ASN VAL SER SEQRES 3 B 166 LEU ALA LYS ALA LYS GLY VAL TRP SER THR LEU PRO VAL SEQRES 4 B 166 ASN GLU LYS LYS LEU ASN LEU ALA PHE ARG SER ALA ARG SEQRES 5 B 166 SER VAL ILE LEU ILE PHE SER VAL ARG GLU SER GLY LYS SEQRES 6 B 166 PHE GLN GLY PHE ALA ARG LEU SER SER GLU SER HIS HIS SEQRES 7 B 166 GLY GLY SER PRO ILE HIS TRP VAL LEU PRO ALA GLY MET SEQRES 8 B 166 SER ALA LYS MET LEU GLY GLY VAL PHE LYS ILE ASP TRP SEQRES 9 B 166 ILE CYS ARG ARG GLU LEU PRO PHE THR LYS SER ALA HIS SEQRES 10 B 166 LEU THR ASN PRO TRP ASN GLU HIS LYS PRO VAL LYS ILE SEQRES 11 B 166 GLY ARG ASP GLY GLN GLU ILE GLU LEU GLU CYS GLY THR SEQRES 12 B 166 GLN LEU CYS LEU LEU PHE PRO PRO ASP GLU SER ILE ASP SEQRES 13 B 166 LEU TYR GLN VAL ILE HIS LYS MET ARG HIS HET UNX A 601 1 HET UNX A 602 1 HET UNX A 603 1 HET UNX A 604 1 HET UNX A 605 1 HET SO4 B 601 5 HET UNX B 602 1 HET UNX B 603 1 HET UNX B 604 1 HET UNX B 605 1 HET UNX B 606 1 HET UNX B 607 1 HETNAM UNX UNKNOWN ATOM OR ION HETNAM SO4 SULFATE ION FORMUL 3 UNX 11(X) FORMUL 8 SO4 O4 S 2- FORMUL 15 HOH *158(H2 O) HELIX 1 1 THR A 345 GLN A 353 1 9 HELIX 2 2 ASN A 364 GLY A 375 1 12 HELIX 3 3 LEU A 380 ALA A 394 1 15 HELIX 4 4 THR A 456 ALA A 459 5 4 HELIX 5 5 ASN A 463 GLU A 467 5 5 HELIX 6 6 GLU A 481 PHE A 492 1 12 HELIX 7 7 ASP A 499 HIS A 505 1 7 HELIX 8 8 THR B 345 GLN B 353 1 9 HELIX 9 9 ASN B 364 GLY B 375 1 12 HELIX 10 10 LEU B 380 ALA B 394 1 15 HELIX 11 11 THR B 456 ALA B 459 5 4 HELIX 12 12 ASN B 463 GLU B 467 5 5 HELIX 13 13 GLU B 481 PHE B 492 1 12 HELIX 14 14 LEU B 500 LYS B 506 1 7 SHEET 1 A 4 VAL A 376 SER A 378 0 SHEET 2 A 4 VAL A 442 CYS A 449 -1 O PHE A 443 N TRP A 377 SHEET 3 A 4 LYS A 408 LEU A 415 -1 N ARG A 414 O ASP A 446 SHEET 4 A 4 LEU A 453 PRO A 454 -1 O LEU A 453 N PHE A 409 SHEET 1 B 6 VAL A 376 SER A 378 0 SHEET 2 B 6 VAL A 442 CYS A 449 -1 O PHE A 443 N TRP A 377 SHEET 3 B 6 LYS A 408 LEU A 415 -1 N ARG A 414 O ASP A 446 SHEET 4 B 6 VAL A 397 VAL A 403 -1 N VAL A 397 O LEU A 415 SHEET 5 B 6 ARG A 356 SER A 362 1 N ARG A 356 O ILE A 398 SHEET 6 B 6 GLU A 479 ILE A 480 -1 O ILE A 480 N PHE A 357 SHEET 1 C 6 VAL B 376 TRP B 377 0 SHEET 2 C 6 PHE B 443 CYS B 449 -1 O PHE B 443 N TRP B 377 SHEET 3 C 6 GLY B 411 LEU B 415 -1 N ARG B 414 O ASP B 446 SHEET 4 C 6 SER B 396 VAL B 403 -1 N LEU B 399 O ALA B 413 SHEET 5 C 6 ALA B 355 SER B 362 1 N ILE B 360 O ILE B 400 SHEET 6 C 6 GLU B 479 ILE B 480 -1 O ILE B 480 N PHE B 357 SHEET 1 D 2 LYS B 408 PHE B 409 0 SHEET 2 D 2 LEU B 453 PRO B 454 -1 O LEU B 453 N PHE B 409 SITE 1 AC1 3 ARG B 451 GLU B 452 HOH B 746 CRYST1 39.264 103.026 41.585 90.00 105.86 90.00 P 1 21 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 0.025469 0.000000 0.007233 0.00000 SCALE2 0.000000 0.009706 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024998 0.00000