HEADER TRANSFERASE 14-MAR-17 5NFJ TITLE CRYSTAL STRUCTURE OF THE METHYLTRANSFERASE SUBUNIT OF HUMAN TITLE 2 MITOCHONDRIAL RIBONUCLEASE P (MRPP1) BOUND TO S-ADENOSYL-METHIONINE TITLE 3 (SAM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL RIBONUCLEASE P PROTEIN 1; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: MITOCHONDRIAL RNASE P PROTEIN 1,HBV PRE-S2 TRANS-REGULATED COMPND 5 PROTEIN 2,RNA (GUANINE-9-)-METHYLTRANSFERASE DOMAIN-CONTAINING COMPND 6 PROTEIN 1,RENAL CARCINOMA ANTIGEN NY-REN-49,TRNA METHYLTRANSFERASE 10 COMPND 7 HOMOLOG C; COMPND 8 EC: 2.1.1.-; COMPND 9 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: TRMT10C, MRPP1, RG9MTD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS SPOUT, METHYLATION, TRNA, TRMT10C, STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, SGC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.OERUM,J.KOPEC,F.FITZPATRICK,J.A.NEWMAN,R.CHALK,L.SHRESTHA, AUTHOR 2 M.FAIRHEAD,R.TALON,N.BURGESS-BROWN,F.VON DELFT,C.ARROWSMITH, AUTHOR 3 C.EDWARDS,C.BOUNTRA,U.OPPERMANN,W.W.YUE,STRUCTURAL GENOMICS AUTHOR 4 CONSORTIUM (SGC) REVDAT 2 16-OCT-19 5NFJ 1 REMARK REVDAT 1 16-MAY-18 5NFJ 0 JRNL AUTH S.OERUM,J.KOPEC,F.FITZPATRICK,J.A.NEWMAN,U.OPPERMANN,W.W.YUE JRNL TITL CRYSTAL STRUCTURE OF THE METHYLTRANSFERASE SUBUNIT OF HUMAN JRNL TITL 2 MITOCHONDRIAL RIBONUCLEASE P (MRPP1) BOUND TO JRNL TITL 3 S-ADENOSYL-METHIONINE (SAM) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 82.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 67692 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3570 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) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5015 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE SET COUNT : 262 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4387 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 139 REMARK 3 SOLVENT ATOMS : 217 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.37000 REMARK 3 B22 (A**2) : 1.37000 REMARK 3 B33 (A**2) : -2.74000 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): 0.116 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.109 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.108 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.148 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4641 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4346 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6264 ; 1.878 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10111 ; 1.074 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 536 ; 6.993 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 219 ;39.296 ;24.521 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 852 ;13.894 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;17.549 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 696 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4949 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 923 ; 0.002 ; 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): 2144 ; 4.672 ; 5.193 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2144 ; 4.671 ; 5.193 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2671 ; 6.453 ; 7.753 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2672 ; 6.452 ; 7.752 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2497 ; 5.495 ; 5.774 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2497 ; 5.495 ; 5.774 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3591 ; 7.903 ; 8.433 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4989 ; 9.914 ;59.822 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4958 ; 9.916 ;59.704 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 : NULL 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 5NFJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200004015. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92820 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67692 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 82.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: DIAMONDS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL SOLUTION: 12% PEG 1000, 28% REMARK 280 GLYCEROL, 1.5%(W/V) PEG 3350 CRYO: 25% PROPYLENE GLYCOL PROTEIN REMARK 280 CONCENTRATION: 11 MG/ML, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 74.31000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 111.46500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.15500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 LYS A 380 REMARK 465 HIS A 381 REMARK 465 THR A 382 REMARK 465 GLY A 383 REMARK 465 PHE A 384 REMARK 465 LEU A 385 REMARK 465 GLU A 386 REMARK 465 ILE A 387 REMARK 465 SER A 388 REMARK 465 GLN A 389 REMARK 465 HIS A 390 REMARK 465 SER A 391 REMARK 465 GLN A 392 REMARK 465 GLU A 393 REMARK 465 PHE A 394 REMARK 465 ILE A 395 REMARK 465 ASN A 396 REMARK 465 ARG A 397 REMARK 465 LEU A 398 REMARK 465 LYS A 399 REMARK 465 LYS A 400 REMARK 465 ALA A 401 REMARK 465 LYS A 402 REMARK 465 THR A 403 REMARK 465 ARG B 379 REMARK 465 LYS B 380 REMARK 465 HIS B 381 REMARK 465 THR B 382 REMARK 465 GLY B 383 REMARK 465 PHE B 384 REMARK 465 LEU B 385 REMARK 465 GLU B 386 REMARK 465 ILE B 387 REMARK 465 SER B 388 REMARK 465 GLN B 389 REMARK 465 HIS B 390 REMARK 465 SER B 391 REMARK 465 GLN B 392 REMARK 465 GLU B 393 REMARK 465 PHE B 394 REMARK 465 ILE B 395 REMARK 465 ASN B 396 REMARK 465 ARG B 397 REMARK 465 LEU B 398 REMARK 465 LYS B 399 REMARK 465 LYS B 400 REMARK 465 ALA B 401 REMARK 465 LYS B 402 REMARK 465 THR B 403 REMARK 465 LYS C 380 REMARK 465 HIS C 381 REMARK 465 THR C 382 REMARK 465 GLY C 383 REMARK 465 PHE C 384 REMARK 465 LEU C 385 REMARK 465 GLU C 386 REMARK 465 ILE C 387 REMARK 465 SER C 388 REMARK 465 GLN C 389 REMARK 465 HIS C 390 REMARK 465 SER C 391 REMARK 465 GLN C 392 REMARK 465 GLU C 393 REMARK 465 PHE C 394 REMARK 465 ILE C 395 REMARK 465 ASN C 396 REMARK 465 ARG C 397 REMARK 465 LEU C 398 REMARK 465 LYS C 399 REMARK 465 LYS C 400 REMARK 465 ALA C 401 REMARK 465 LYS C 402 REMARK 465 THR C 403 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 LYS A 315 CE NZ REMARK 470 LYS B 268 CG CD CE NZ REMARK 470 LYS B 315 CE NZ REMARK 470 GLN C 343 CG CD OE1 NE2 REMARK 470 ARG C 379 CG CD NE CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG C 261 CA CB CG CD NE CZ NH1 REMARK 480 ARG C 261 NH2 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 N LEU A 220 O HOH A 601 2.03 REMARK 500 O ARG A 217 O HOH A 601 2.04 REMARK 500 SG CYS B 362 O2 EDO B 506 2.10 REMARK 500 OH TYR B 341 O HOH B 601 2.12 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 235 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 MET A 317 CG - SD - CE ANGL. DEV. = 10.0 DEGREES REMARK 500 ASP B 239 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP B 293 CB - CG - OD2 ANGL. DEV. = 5.8 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 MET A 209 32.79 -93.23 REMARK 500 ASP A 251 18.43 59.22 REMARK 500 SER A 316 12.13 59.03 REMARK 500 TRP A 344 -163.81 57.62 REMARK 500 ALA B 210 30.56 -87.68 REMARK 500 GLN B 263 -134.97 62.94 REMARK 500 SER B 316 1.69 58.56 REMARK 500 LEU B 342 89.14 -151.37 REMARK 500 GLN B 343 -75.08 -62.62 REMARK 500 GLU B 345 -28.77 78.70 REMARK 500 ASN B 348 111.46 133.60 REMARK 500 ASP C 251 18.61 55.52 REMARK 500 GLN C 263 -134.36 57.38 REMARK 500 LEU C 342 42.34 -141.16 REMARK 500 ASN C 365 30.49 -90.84 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 SAM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM C 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 502 DBREF 5NFJ A 203 403 UNP Q7L0Y3 MRRP1_HUMAN 203 403 DBREF 5NFJ B 203 403 UNP Q7L0Y3 MRRP1_HUMAN 203 403 DBREF 5NFJ C 203 403 UNP Q7L0Y3 MRRP1_HUMAN 203 403 SEQADV 5NFJ MET A 202 UNP Q7L0Y3 INITIATING METHIONINE SEQADV 5NFJ MET B 202 UNP Q7L0Y3 INITIATING METHIONINE SEQADV 5NFJ MET C 202 UNP Q7L0Y3 INITIATING METHIONINE SEQRES 1 A 202 MET GLN PRO LEU VAL PHE ASP MET ALA TYR GLU ASN TYR SEQRES 2 A 202 MET LYS ARG LYS GLU LEU GLN ASN THR VAL SER GLN LEU SEQRES 3 A 202 LEU GLU SER GLU GLY TRP ASN ARG ARG ASN VAL ASP PRO SEQRES 4 A 202 PHE HIS ILE TYR PHE CYS ASN LEU LYS ILE ASP GLY ALA SEQRES 5 A 202 LEU HIS ARG GLU LEU VAL LYS ARG TYR GLN GLU LYS TRP SEQRES 6 A 202 ASP LYS LEU LEU LEU THR SER THR GLU LYS SER HIS VAL SEQRES 7 A 202 ASP LEU PHE PRO LYS ASP SER ILE ILE TYR LEU THR ALA SEQRES 8 A 202 ASP SER PRO ASN VAL MET THR THR PHE ARG HIS ASP LYS SEQRES 9 A 202 VAL TYR VAL ILE GLY SER PHE VAL ASP LYS SER MET GLN SEQRES 10 A 202 PRO GLY THR SER LEU ALA LYS ALA LYS ARG LEU ASN LEU SEQRES 11 A 202 ALA THR GLU CYS LEU PRO LEU ASP LYS TYR LEU GLN TRP SEQRES 12 A 202 GLU ILE GLY ASN LYS ASN LEU THR LEU ASP GLN MET ILE SEQRES 13 A 202 ARG ILE LEU LEU CYS LEU LYS ASN ASN GLY ASN TRP GLN SEQRES 14 A 202 GLU ALA LEU GLN PHE VAL PRO LYS ARG LYS HIS THR GLY SEQRES 15 A 202 PHE LEU GLU ILE SER GLN HIS SER GLN GLU PHE ILE ASN SEQRES 16 A 202 ARG LEU LYS LYS ALA LYS THR SEQRES 1 B 202 MET GLN PRO LEU VAL PHE ASP MET ALA TYR GLU ASN TYR SEQRES 2 B 202 MET LYS ARG LYS GLU LEU GLN ASN THR VAL SER GLN LEU SEQRES 3 B 202 LEU GLU SER GLU GLY TRP ASN ARG ARG ASN VAL ASP PRO SEQRES 4 B 202 PHE HIS ILE TYR PHE CYS ASN LEU LYS ILE ASP GLY ALA SEQRES 5 B 202 LEU HIS ARG GLU LEU VAL LYS ARG TYR GLN GLU LYS TRP SEQRES 6 B 202 ASP LYS LEU LEU LEU THR SER THR GLU LYS SER HIS VAL SEQRES 7 B 202 ASP LEU PHE PRO LYS ASP SER ILE ILE TYR LEU THR ALA SEQRES 8 B 202 ASP SER PRO ASN VAL MET THR THR PHE ARG HIS ASP LYS SEQRES 9 B 202 VAL TYR VAL ILE GLY SER PHE VAL ASP LYS SER MET GLN SEQRES 10 B 202 PRO GLY THR SER LEU ALA LYS ALA LYS ARG LEU ASN LEU SEQRES 11 B 202 ALA THR GLU CYS LEU PRO LEU ASP LYS TYR LEU GLN TRP SEQRES 12 B 202 GLU ILE GLY ASN LYS ASN LEU THR LEU ASP GLN MET ILE SEQRES 13 B 202 ARG ILE LEU LEU CYS LEU LYS ASN ASN GLY ASN TRP GLN SEQRES 14 B 202 GLU ALA LEU GLN PHE VAL PRO LYS ARG LYS HIS THR GLY SEQRES 15 B 202 PHE LEU GLU ILE SER GLN HIS SER GLN GLU PHE ILE ASN SEQRES 16 B 202 ARG LEU LYS LYS ALA LYS THR SEQRES 1 C 202 MET GLN PRO LEU VAL PHE ASP MET ALA TYR GLU ASN TYR SEQRES 2 C 202 MET LYS ARG LYS GLU LEU GLN ASN THR VAL SER GLN LEU SEQRES 3 C 202 LEU GLU SER GLU GLY TRP ASN ARG ARG ASN VAL ASP PRO SEQRES 4 C 202 PHE HIS ILE TYR PHE CYS ASN LEU LYS ILE ASP GLY ALA SEQRES 5 C 202 LEU HIS ARG GLU LEU VAL LYS ARG TYR GLN GLU LYS TRP SEQRES 6 C 202 ASP LYS LEU LEU LEU THR SER THR GLU LYS SER HIS VAL SEQRES 7 C 202 ASP LEU PHE PRO LYS ASP SER ILE ILE TYR LEU THR ALA SEQRES 8 C 202 ASP SER PRO ASN VAL MET THR THR PHE ARG HIS ASP LYS SEQRES 9 C 202 VAL TYR VAL ILE GLY SER PHE VAL ASP LYS SER MET GLN SEQRES 10 C 202 PRO GLY THR SER LEU ALA LYS ALA LYS ARG LEU ASN LEU SEQRES 11 C 202 ALA THR GLU CYS LEU PRO LEU ASP LYS TYR LEU GLN TRP SEQRES 12 C 202 GLU ILE GLY ASN LYS ASN LEU THR LEU ASP GLN MET ILE SEQRES 13 C 202 ARG ILE LEU LEU CYS LEU LYS ASN ASN GLY ASN TRP GLN SEQRES 14 C 202 GLU ALA LEU GLN PHE VAL PRO LYS ARG LYS HIS THR GLY SEQRES 15 C 202 PHE LEU GLU ILE SER GLN HIS SER GLN GLU PHE ILE ASN SEQRES 16 C 202 ARG LEU LYS LYS ALA LYS THR HET SAM A 501 27 HET GOL A 502 6 HET GOL A 503 6 HET GOL A 504 6 HET EDO A 505 4 HET EDO A 506 4 HET SAM B 501 27 HET GOL B 502 6 HET GOL B 503 6 HET GOL B 504 6 HET EDO B 505 4 HET EDO B 506 4 HET SAM C 501 27 HET GOL C 502 6 HETNAM SAM S-ADENOSYLMETHIONINE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 SAM 3(C15 H22 N6 O5 S) FORMUL 5 GOL 7(C3 H8 O3) FORMUL 8 EDO 4(C2 H6 O2) FORMUL 18 HOH *217(H2 O) HELIX 1 AA1 TYR A 211 MET A 215 5 5 HELIX 2 AA2 LYS A 216 ASN A 237 1 22 HELIX 3 AA3 GLY A 252 TYR A 262 1 11 HELIX 4 AA4 TYR A 262 LEU A 269 1 8 HELIX 5 AA5 SER A 277 PHE A 282 1 6 HELIX 6 AA6 PRO A 283 ASP A 285 5 3 HELIX 7 AA7 GLY A 320 ARG A 328 1 9 HELIX 8 AA8 PRO A 337 LEU A 342 1 6 HELIX 9 AA9 THR A 352 ASN A 365 1 14 HELIX 10 AB1 ASN A 368 LEU A 373 1 6 HELIX 11 AB2 GLN A 374 VAL A 376 5 3 HELIX 12 AB3 TYR B 211 MET B 215 5 5 HELIX 13 AB4 LYS B 216 ARG B 236 1 21 HELIX 14 AB5 GLY B 252 GLN B 263 1 12 HELIX 15 AB6 GLU B 264 LEU B 269 5 6 HELIX 16 AB7 SER B 277 PHE B 282 1 6 HELIX 17 AB8 PRO B 283 ASP B 285 5 3 HELIX 18 AB9 GLY B 320 LEU B 329 1 10 HELIX 19 AC1 PRO B 337 LEU B 342 1 6 HELIX 20 AC2 THR B 352 GLY B 367 1 16 HELIX 21 AC3 ASN B 368 LEU B 373 1 6 HELIX 22 AC4 GLN B 374 VAL B 376 5 3 HELIX 23 AC5 TYR C 211 MET C 215 5 5 HELIX 24 AC6 LYS C 216 ARG C 236 1 21 HELIX 25 AC7 GLY C 252 GLN C 263 1 12 HELIX 26 AC8 GLU C 264 LEU C 269 5 6 HELIX 27 AC9 SER C 277 PHE C 282 1 6 HELIX 28 AD1 PRO C 283 ASP C 285 5 3 HELIX 29 AD2 GLY C 320 LEU C 329 1 10 HELIX 30 AD3 PRO C 337 LEU C 342 1 6 HELIX 31 AD4 THR C 352 ASN C 365 1 14 HELIX 32 AD5 ASN C 368 LEU C 373 1 6 HELIX 33 AD6 GLN C 374 VAL C 376 5 3 SHEET 1 AA1 6 THR A 272 SER A 273 0 SHEET 2 AA1 6 HIS A 242 CYS A 246 1 N PHE A 245 O THR A 272 SHEET 3 AA1 6 PRO A 204 ASP A 208 1 N PHE A 207 O TYR A 244 SHEET 4 AA1 6 VAL A 306 GLY A 310 1 O ILE A 309 N ASP A 208 SHEET 5 AA1 6 ILE A 287 LEU A 290 1 N LEU A 290 O VAL A 308 SHEET 6 AA1 6 THR A 333 GLU A 334 1 O GLU A 334 N TYR A 289 SHEET 1 AA2 6 THR B 272 SER B 273 0 SHEET 2 AA2 6 HIS B 242 CYS B 246 1 N PHE B 245 O THR B 272 SHEET 3 AA2 6 PRO B 204 ASP B 208 1 N PHE B 207 O TYR B 244 SHEET 4 AA2 6 VAL B 306 GLY B 310 1 O ILE B 309 N ASP B 208 SHEET 5 AA2 6 ILE B 287 LEU B 290 1 N LEU B 290 O VAL B 308 SHEET 6 AA2 6 ALA B 332 GLU B 334 1 O ALA B 332 N TYR B 289 SHEET 1 AA3 6 THR C 272 SER C 273 0 SHEET 2 AA3 6 HIS C 242 CYS C 246 1 N PHE C 245 O THR C 272 SHEET 3 AA3 6 PRO C 204 ASP C 208 1 N LEU C 205 O TYR C 244 SHEET 4 AA3 6 VAL C 306 GLY C 310 1 O ILE C 309 N ASP C 208 SHEET 5 AA3 6 ILE C 287 LEU C 290 1 N LEU C 290 O VAL C 308 SHEET 6 AA3 6 ALA C 332 GLU C 334 1 O ALA C 332 N TYR C 289 SITE 1 AC1 19 LEU A 290 THR A 291 ALA A 292 ILE A 309 SITE 2 AC1 19 GLY A 310 PHE A 312 ASP A 314 GLN A 318 SITE 3 AC1 19 THR A 321 SER A 322 LEU A 336 LEU A 338 SITE 4 AC1 19 LYS A 349 ASN A 350 LEU A 351 MET A 356 SITE 5 AC1 19 HOH A 607 HOH A 613 HOH A 616 SITE 1 AC2 4 THR A 299 PHE A 301 ASN A 368 TRP A 369 SITE 1 AC3 6 MET A 298 THR A 299 THR A 300 ARG A 302 SITE 2 AC3 6 GLU A 334 HOH A 622 SITE 1 AC4 4 ARG A 236 MET C 215 LYS C 216 LEU C 220 SITE 1 AC5 6 GLN A 226 THR A 352 ASP A 354 GLN A 355 SITE 2 AC5 6 HOH A 608 HOH A 623 SITE 1 AC6 1 VAL A 279 SITE 1 AC7 20 LEU B 290 THR B 291 ALA B 292 ILE B 309 SITE 2 AC7 20 GLY B 310 PHE B 312 ASP B 314 GLN B 318 SITE 3 AC7 20 THR B 321 SER B 322 CYS B 335 LEU B 336 SITE 4 AC7 20 LYS B 349 ASN B 350 LEU B 351 MET B 356 SITE 5 AC7 20 HOH B 609 HOH B 620 HOH B 644 HOH B 660 SITE 1 AC8 3 VAL B 279 ASP B 280 PRO B 283 SITE 1 AC9 6 VAL A 238 PRO A 240 ASN B 213 MET B 215 SITE 2 AC9 6 ARG C 217 GLN C 221 SITE 1 AD1 5 THR B 299 THR B 300 PHE B 301 GLY B 367 SITE 2 AD1 5 TRP B 369 SITE 1 AD2 5 ILE B 250 HIS B 255 TRP B 266 SER B 273 SITE 2 AD2 5 HOH B 625 SITE 1 AD3 3 CYS B 362 ASN B 366 GLU B 371 SITE 1 AD4 20 LEU C 290 THR C 291 ALA C 292 ILE C 309 SITE 2 AD4 20 GLY C 310 PHE C 312 ASP C 314 GLN C 318 SITE 3 AD4 20 THR C 321 SER C 322 CYS C 335 LEU C 336 SITE 4 AD4 20 LYS C 349 ASN C 350 LEU C 351 MET C 356 SITE 5 AD4 20 HOH C 610 HOH C 615 HOH C 625 HOH C 629 SITE 1 AD5 4 THR C 300 PHE C 301 GLY C 367 TRP C 369 CRYST1 82.640 82.640 148.620 90.00 90.00 90.00 P 43 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 0.012101 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012101 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006729 0.00000