PDB Short entry for 6DUB HEADER TRANSFERASE 20-JUN-18 6DUB TITLE CRYSTAL STRUCTURE OF A METHYLTRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA N-TERMINAL PROTEIN METHYLTRANSFERASE 1B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 58-278; COMPND 5 SYNONYM: METHYLTRANSFERASE-LIKE PROTEIN 11B, X-PRO-LYS N-TERMINAL COMPND 6 PROTEIN METHYLTRANSFERASE 1B, NTM1B; COMPND 7 EC: 2.1.1.299; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RCC1; COMPND 11 CHAIN: E, F; COMPND 12 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: METTL11B, C1ORF184, NRMT2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-V3R; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MKH8SUMO; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS METHYLTRANSFERASE, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.DONG,W.TEMPEL,Y.LI,C.BOUNTRA,C.H.ARROWSMITH,A.M.EDWARDS,J.MIN, AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 2 28-NOV-18 6DUB 1 JRNL REVDAT 1 25-JUL-18 6DUB 0 JRNL AUTH C.DONG,G.DONG,L.LI,L.ZHU,W.TEMPEL,Y.LIU,R.HUANG,J.MIN JRNL TITL AN ASPARAGINE/GLYCINE SWITCH GOVERNS PRODUCT SPECIFICITY OF JRNL TITL 2 HUMAN N-TERMINAL METHYLTRANSFERASE NTMT2. JRNL REF COMMUN BIOL V. 1 183 2018 JRNL REFN ESSN 2399-3642 JRNL PMID 30417120 JRNL DOI 10.1038/S42003-018-0196-2 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0218 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 145394 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.300 REMARK 3 FREE R VALUE TEST SET COUNT : 4983 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10825 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3509 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 130 REMARK 3 SOLVENT ATOMS : 314 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.35000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : 0.71000 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): 0.037 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.037 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.023 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.144 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3888 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3687 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5291 ; 1.823 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8584 ; 0.921 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 506 ; 6.176 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;32.412 ;23.494 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 692 ;11.493 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;12.089 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 595 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4303 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 806 ; 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): 1883 ; 2.024 ; 1.458 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1884 ; 2.024 ; 1.458 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2361 ; 2.706 ; 2.208 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): 7574 ; 2.700 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 223 ;18.025 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7623 ; 8.282 ; 5.000 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6DUB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000233578. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 150535 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 31.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.97300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 5E1D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG2000, 0.1 M POTASSIUM REMARK 280 THIOCYANATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 131.02900 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 196.54350 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 65.51450 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 B 57 REMARK 465 THR B 58 REMARK 465 SER B 59 REMARK 465 GLN B 60 REMARK 465 ALA E 6 REMARK 465 ALA F 6 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 GLN A 60 CG CD OE1 NE2 REMARK 470 ILE A 62 CG1 CG2 CD1 REMARK 470 ASP A 118 OD1 OD2 REMARK 470 GLU A 149 CD OE1 OE2 REMARK 470 LYS A 162 CE NZ REMARK 470 GLU A 167 CD OE1 OE2 REMARK 470 LYS A 199 CD CE NZ REMARK 470 ARG A 209 NH1 NH2 REMARK 470 GLU A 227 OE1 OE2 REMARK 470 ASP A 263 CG OD1 OD2 REMARK 470 GLU A 267 CD OE1 OE2 REMARK 470 VAL B 61 N CB CG1 CG2 REMARK 470 LYS B 103 NZ REMARK 470 LYS B 162 CE NZ REMARK 470 LYS B 165 CE NZ REMARK 470 GLU B 227 CG CD OE1 OE2 REMARK 470 ILE E 5 C O CB CG1 CG2 CD1 REMARK 470 ILE F 5 C O CB CG1 CG2 CD1 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 NH2 ARG A 246 OE1 GLN A 259 2.15 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 NH2 ARG A 246 UNK UNX B 311 4665 2.15 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 B 250 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 250 NE - CZ - NH2 ANGL. DEV. = -4.4 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 SER B 236 63.46 63.05 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 SAH A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAH B 301 DBREF 6DUB A 58 278 UNP Q5VVY1 NTM1B_HUMAN 58 278 DBREF 6DUB B 58 278 UNP Q5VVY1 NTM1B_HUMAN 58 278 DBREF 6DUB E 1 6 PDB 6DUB 6DUB 1 6 DBREF 6DUB F 1 6 PDB 6DUB 6DUB 1 6 SEQADV 6DUB GLY A 57 UNP Q5VVY1 EXPRESSION TAG SEQADV 6DUB GLY B 57 UNP Q5VVY1 EXPRESSION TAG SEQRES 1 A 222 GLY THR SER GLN VAL ILE ASN GLY GLU MET GLN PHE TYR SEQRES 2 A 222 ALA ARG ALA LYS LEU PHE TYR GLN GLU VAL PRO ALA THR SEQRES 3 A 222 GLU GLU GLY MET MET GLY ASN PHE ILE GLU LEU SER SER SEQRES 4 A 222 PRO ASP ILE GLN ALA SER GLN LYS PHE LEU ARG LYS PHE SEQRES 5 A 222 VAL GLY GLY PRO GLY ARG ALA GLY THR ASP CYS ALA LEU SEQRES 6 A 222 ASP CYS GLY SER GLY ILE GLY ARG VAL SER LYS HIS VAL SEQRES 7 A 222 LEU LEU PRO VAL PHE ASN SER VAL GLU LEU VAL ASP MET SEQRES 8 A 222 MET GLU SER PHE LEU LEU GLU ALA GLN ASN TYR LEU GLN SEQRES 9 A 222 VAL LYS GLY ASP LYS VAL GLU SER TYR HIS CYS TYR SER SEQRES 10 A 222 LEU GLN GLU PHE THR PRO PRO PHE ARG ARG TYR ASP VAL SEQRES 11 A 222 ILE TRP ILE GLN TRP VAL SER GLY HIS LEU THR ASP LYS SEQRES 12 A 222 ASP LEU LEU ALA PHE LEU SER ARG CYS ARG ASP GLY LEU SEQRES 13 A 222 LYS GLU ASN GLY ILE ILE ILE LEU LYS ASP ASN VAL ALA SEQRES 14 A 222 ARG GLU GLY CYS ILE LEU ASP LEU SER ASP SER SER VAL SEQRES 15 A 222 THR ARG ASP MET ASP ILE LEU ARG SER LEU ILE ARG LYS SEQRES 16 A 222 SER GLY LEU VAL VAL LEU GLY GLN GLU LYS GLN ASP GLY SEQRES 17 A 222 PHE PRO GLU GLN CYS ILE PRO VAL TRP MET PHE ALA LEU SEQRES 18 A 222 HIS SEQRES 1 B 222 GLY THR SER GLN VAL ILE ASN GLY GLU MET GLN PHE TYR SEQRES 2 B 222 ALA ARG ALA LYS LEU PHE TYR GLN GLU VAL PRO ALA THR SEQRES 3 B 222 GLU GLU GLY MET MET GLY ASN PHE ILE GLU LEU SER SER SEQRES 4 B 222 PRO ASP ILE GLN ALA SER GLN LYS PHE LEU ARG LYS PHE SEQRES 5 B 222 VAL GLY GLY PRO GLY ARG ALA GLY THR ASP CYS ALA LEU SEQRES 6 B 222 ASP CYS GLY SER GLY ILE GLY ARG VAL SER LYS HIS VAL SEQRES 7 B 222 LEU LEU PRO VAL PHE ASN SER VAL GLU LEU VAL ASP MET SEQRES 8 B 222 MET GLU SER PHE LEU LEU GLU ALA GLN ASN TYR LEU GLN SEQRES 9 B 222 VAL LYS GLY ASP LYS VAL GLU SER TYR HIS CYS TYR SER SEQRES 10 B 222 LEU GLN GLU PHE THR PRO PRO PHE ARG ARG TYR ASP VAL SEQRES 11 B 222 ILE TRP ILE GLN TRP VAL SER GLY HIS LEU THR ASP LYS SEQRES 12 B 222 ASP LEU LEU ALA PHE LEU SER ARG CYS ARG ASP GLY LEU SEQRES 13 B 222 LYS GLU ASN GLY ILE ILE ILE LEU LYS ASP ASN VAL ALA SEQRES 14 B 222 ARG GLU GLY CYS ILE LEU ASP LEU SER ASP SER SER VAL SEQRES 15 B 222 THR ARG ASP MET ASP ILE LEU ARG SER LEU ILE ARG LYS SEQRES 16 B 222 SER GLY LEU VAL VAL LEU GLY GLN GLU LYS GLN ASP GLY SEQRES 17 B 222 PHE PRO GLU GLN CYS ILE PRO VAL TRP MET PHE ALA LEU SEQRES 18 B 222 HIS SEQRES 1 E 6 5JP PRO LYS ARG ILE ALA SEQRES 1 F 6 5JP PRO LYS ARG ILE ALA HET 5JP E 1 7 HET 5JP F 1 7 HET SAH A 301 35 HET GOL A 302 10 HET GOL A 303 8 HET UNX A 304 1 HET UNX A 305 1 HET UNX A 306 1 HET UNX A 307 1 HET UNX A 308 1 HET UNX A 309 1 HET UNX A 310 1 HET UNX A 311 1 HET UNX A 312 1 HET UNX A 313 1 HET UNX A 314 1 HET UNX A 315 1 HET UNX A 316 1 HET UNX A 317 1 HET UNX A 318 1 HET UNX A 319 1 HET UNX A 320 1 HET UNX A 321 1 HET UNX A 322 1 HET UNX A 323 1 HET UNX A 324 1 HET UNX A 325 1 HET UNX A 326 1 HET UNX A 327 1 HET UNX A 328 1 HET UNX A 329 1 HET UNX A 330 1 HET UNX A 331 1 HET UNX A 332 1 HET UNX A 333 1 HET UNX A 334 1 HET UNX A 335 1 HET UNX A 336 1 HET UNX A 337 1 HET SAH B 301 35 HET GOL B 302 6 HET UNX B 303 1 HET UNX B 304 1 HET UNX B 305 1 HET UNX B 306 1 HET UNX B 307 1 HET UNX B 308 1 HET UNX B 309 1 HET UNX B 310 1 HET UNX B 311 1 HET UNX B 312 1 HET UNX B 313 1 HET UNX B 314 1 HET UNX B 315 1 HET UNX B 316 1 HET UNX B 317 1 HET UNX B 318 1 HET UNX B 319 1 HET UNX B 320 1 HET UNX B 321 1 HET UNX B 322 1 HET UNX B 323 1 HET UNX B 324 1 HET UNX E 101 1 HET UNX E 102 1 HET UNX E 103 1 HET UNX F 101 1 HETNAM 5JP N-METHYL-L-SERINE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM GOL GLYCEROL HETNAM UNX UNKNOWN ATOM OR ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 5JP 2(C4 H9 N O3) FORMUL 5 SAH 2(C14 H20 N6 O5 S) FORMUL 6 GOL 3(C3 H8 O3) FORMUL 8 UNX 60(X) FORMUL 70 HOH *314(H2 O) HELIX 1 AA1 ASN A 63 GLN A 77 1 15 HELIX 2 AA2 THR A 82 MET A 87 1 6 HELIX 3 AA3 PHE A 90 GLU A 92 5 3 HELIX 4 AA4 LEU A 93 ARG A 106 1 14 HELIX 5 AA5 GLY A 128 VAL A 134 1 7 HELIX 6 AA6 MET A 148 LEU A 159 1 12 HELIX 7 AA7 GLN A 160 ASP A 164 5 5 HELIX 8 AA8 SER A 173 PHE A 177 5 5 HELIX 9 AA9 VAL A 192 LEU A 196 5 5 HELIX 10 AB1 THR A 197 GLY A 211 1 15 HELIX 11 AB2 MET A 242 SER A 252 1 11 HELIX 12 AB3 ASN B 63 GLN B 77 1 15 HELIX 13 AB4 THR B 82 MET B 87 1 6 HELIX 14 AB5 PHE B 90 GLU B 92 5 3 HELIX 15 AB6 LEU B 93 VAL B 109 1 17 HELIX 16 AB7 GLY B 128 VAL B 134 1 7 HELIX 17 AB8 MET B 148 LEU B 159 1 12 HELIX 18 AB9 GLN B 160 ASP B 164 5 5 HELIX 19 AC1 SER B 173 PHE B 177 5 5 HELIX 20 AC2 VAL B 192 LEU B 196 5 5 HELIX 21 AC3 THR B 197 GLY B 211 1 15 HELIX 22 AC4 ASP B 241 SER B 252 1 12 SHEET 1 AA1 7 VAL A 166 CYS A 171 0 SHEET 2 AA1 7 SER A 141 ASP A 146 1 N LEU A 144 O HIS A 170 SHEET 3 AA1 7 CYS A 119 CYS A 123 1 N ASP A 122 O GLU A 143 SHEET 4 AA1 7 TYR A 184 GLN A 190 1 O TRP A 188 N LEU A 121 SHEET 5 AA1 7 LEU A 212 ALA A 225 1 O ILE A 219 N ILE A 189 SHEET 6 AA1 7 SER A 237 ASP A 241 1 O ARG A 240 N ALA A 225 SHEET 7 AA1 7 CYS A 229 ASP A 232 -1 N ASP A 232 O SER A 237 SHEET 1 AA2 7 VAL A 166 CYS A 171 0 SHEET 2 AA2 7 SER A 141 ASP A 146 1 N LEU A 144 O HIS A 170 SHEET 3 AA2 7 CYS A 119 CYS A 123 1 N ASP A 122 O GLU A 143 SHEET 4 AA2 7 TYR A 184 GLN A 190 1 O TRP A 188 N LEU A 121 SHEET 5 AA2 7 LEU A 212 ALA A 225 1 O ILE A 219 N ILE A 189 SHEET 6 AA2 7 VAL A 272 LEU A 277 -1 O LEU A 277 N ILE A 218 SHEET 7 AA2 7 VAL A 256 LYS A 261 -1 N GLY A 258 O ALA A 276 SHEET 1 AA3 7 VAL B 166 CYS B 171 0 SHEET 2 AA3 7 SER B 141 ASP B 146 1 N LEU B 144 O HIS B 170 SHEET 3 AA3 7 CYS B 119 CYS B 123 1 N ASP B 122 O GLU B 143 SHEET 4 AA3 7 TYR B 184 GLN B 190 1 O TRP B 188 N LEU B 121 SHEET 5 AA3 7 LEU B 212 ASN B 223 1 O ILE B 219 N ILE B 189 SHEET 6 AA3 7 VAL B 272 LEU B 277 -1 O LEU B 277 N ILE B 218 SHEET 7 AA3 7 VAL B 256 LYS B 261 -1 N GLY B 258 O ALA B 276 SHEET 1 AA4 2 ILE B 230 ASP B 232 0 SHEET 2 AA4 2 SER B 237 THR B 239 -1 O SER B 237 N ASP B 232 LINK C 5JP E 1 N PRO E 2 1555 1555 1.32 LINK C 5JP F 1 N PRO F 2 1555 1555 1.33 SITE 1 AC1 24 TYR A 76 MET A 86 GLY A 124 SER A 125 SITE 2 AC1 24 GLY A 126 ARG A 129 VAL A 130 ASP A 146 SITE 3 AC1 24 MET A 147 MET A 148 PHE A 151 TYR A 172 SITE 4 AC1 24 SER A 173 LEU A 174 GLN A 175 GLN A 190 SITE 5 AC1 24 TRP A 191 VAL A 192 HIS A 195 LEU A 196 SITE 6 AC1 24 HOH A 440 HOH A 461 HOH A 473 5JP E 1 SITE 1 AC2 9 SER A 95 ILE A 98 GLN A 99 GLN A 102 SITE 2 AC2 9 LEU B 257 GLY B 258 GLN B 259 GLU B 260 SITE 3 AC2 9 HOH B 407 SITE 1 AC3 11 TRP A 191 VAL A 192 GLY A 194 ASP A 222 SITE 2 AC3 11 ASN A 223 ASP A 235 SER A 237 HOH A 410 SITE 3 AC3 11 HOH A 423 5JP E 1 LYS E 3 SITE 1 AC4 23 TYR B 76 MET B 86 GLY B 124 SER B 125 SITE 2 AC4 23 GLY B 126 ARG B 129 VAL B 130 ASP B 146 SITE 3 AC4 23 MET B 147 MET B 148 PHE B 151 TYR B 172 SITE 4 AC4 23 SER B 173 LEU B 174 GLN B 175 GLN B 190 SITE 5 AC4 23 TRP B 191 VAL B 192 HIS B 195 LEU B 196 SITE 6 AC4 23 HOH B 442 HOH B 477 5JP F 1 CRYST1 44.359 44.359 262.058 90.00 90.00 90.00 P 43 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 0.022543 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022543 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003816 0.00000