HEADER RNA BINDING PROTEIN 08-MAY-17 5VQH TITLE CRYSTAL STRUCTURE OF THE EXTENDED TUDOR DOMAIN FROM BMPAPI IN COMPLEX TITLE 2 WITH SDMA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUDOR AND KH DOMAIN-CONTAINING PROTEIN HOMOLOG; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 245-462; COMPND 5 SYNONYM: PARTNER OF PIWIS PROTEIN,BMPAPI; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 3 ORGANISM_COMMON: SILK MOTH; SOURCE 4 ORGANISM_TAXID: 7091; SOURCE 5 GENE: PAPI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BMPAPI, TUDOR, SDMA, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.A.HUBBARD,X.PAN,A.OHTAKI,R.MCNALLY,S.HONDA,Y.KIRINO,R.MURALI REVDAT 5 04-OCT-23 5VQH 1 REMARK REVDAT 4 10-MAR-21 5VQH 1 LINK REVDAT 3 01-JAN-20 5VQH 1 LINK REVDAT 2 13-SEP-17 5VQH 1 REMARK REVDAT 1 14-JUN-17 5VQH 0 JRNL AUTH P.A.HUBBARD,X.PAN,A.OHTAKI,R.MCNALLY,S.HONDA,Y.KIRINO, JRNL AUTH 2 R.MURALI JRNL TITL STRUCTURAL STUDIES OF THE TUDOR DOMAIN FROM THE BOMBYX JRNL TITL 2 HOMOLOG OF DROSOPHILA PAPI: IMPLICATION TO PIRNA BIOGENESIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 17693 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 878 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1347 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.3440 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.3820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3213 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.36000 REMARK 3 B22 (A**2) : -0.36000 REMARK 3 B33 (A**2) : 0.72000 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): 0.448 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.289 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.230 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.461 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3330 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3058 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4530 ; 1.482 ; 1.932 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6971 ; 0.774 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 407 ; 6.949 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 165 ;32.697 ;23.212 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 498 ;15.052 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;20.020 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 496 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3818 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 826 ; 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): 1637 ; 3.108 ; 4.393 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1636 ; 3.106 ; 4.392 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2035 ; 4.773 ; 6.559 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2036 ; 4.772 ; 6.561 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1693 ; 3.611 ; 4.802 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1693 ; 3.603 ; 4.800 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2493 ; 5.839 ; 7.041 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3759 ; 8.179 ;35.396 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3714 ; 8.177 ;35.389 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 5VQH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 MICROMAX-007 HF 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 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18600 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 39.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.53500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: 5VQG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.95 M AMMONIUM SULFATE, 50 MM SODIUM REMARK 280 ACETATE, PH 5.5 AND 5% GLUCOSE., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 112.24000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.01500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.01500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 168.36000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.01500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.01500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.12000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.01500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.01500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 168.36000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.01500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.01500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 56.12000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 112.24000 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 614 LIES ON A SPECIAL POSITION. 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 GLU A -9 REMARK 465 GLY A 134 REMARK 465 GLU A 135 REMARK 465 GLU A 136 REMARK 465 ALA A 137 REMARK 465 VAL A 138 REMARK 465 SER A 139 REMARK 465 PRO A 140 REMARK 465 SER A 141 REMARK 465 GLY A 142 REMARK 465 GLN A 143 REMARK 465 ARG A 144 REMARK 465 TRP A 145 REMARK 465 ALA A 217 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 GLU B -9 REMARK 465 ASN B -8 REMARK 465 LEU B -7 REMARK 465 TYR B -6 REMARK 465 PHE B -5 REMARK 465 GLN B -4 REMARK 465 SER B -3 REMARK 465 ASN B -2 REMARK 465 SER B 133 REMARK 465 GLY B 134 REMARK 465 GLU B 135 REMARK 465 GLU B 136 REMARK 465 ALA B 137 REMARK 465 VAL B 138 REMARK 465 SER B 139 REMARK 465 PRO B 140 REMARK 465 SER B 141 REMARK 465 GLY B 142 REMARK 465 GLN B 143 REMARK 465 ARG B 144 REMARK 465 TRP B 145 REMARK 465 ASP B 146 REMARK 465 THR B 178 REMARK 465 ALA B 179 REMARK 465 THR B 180 REMARK 465 ALA B 181 REMARK 465 GLU B 182 REMARK 465 GLY B 183 REMARK 465 GLU B 184 REMARK 465 LYS B 185 REMARK 465 ASP B 186 REMARK 465 LYS B 187 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 ASN A -8 CG OD1 ND2 REMARK 470 SER A -3 OG REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 LYS A 42 CG CD CE NZ REMARK 470 GLU B 37 CG CD OE1 OE2 REMARK 470 LYS B 41 CG CD CE NZ REMARK 470 LYS B 42 CG CD CE NZ REMARK 470 ARG B 64 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 78 NE CZ NH1 NH2 REMARK 470 SER B 84 OG REMARK 470 ARG B 116 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 130 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 147 CG CD CE NZ REMARK 470 LYS B 176 CG CD CE NZ REMARK 470 LYS B 177 CG CD CE NZ REMARK 470 GLU B 188 CG CD OE1 OE2 REMARK 470 ASP B 199 CG OD1 OD2 REMARK 470 GLU B 200 CG CD OE1 OE2 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 ARG A 15 97.53 -164.21 REMARK 500 HIS A 48 36.88 -140.54 REMARK 500 TYR A 96 -48.23 -139.49 REMARK 500 LYS A 147 -8.82 84.34 REMARK 500 ARG B 15 87.30 -163.44 REMARK 500 TYR B 38 -70.25 -59.97 REMARK 500 HIS B 48 32.51 -141.53 REMARK 500 ASP B 66 -15.33 -143.54 REMARK 500 ASP B 83 88.76 179.24 REMARK 500 THR B 174 -168.16 -126.07 REMARK 500 THR B 198 -128.55 -136.24 REMARK 500 GLU B 202 82.87 -173.10 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 2MR A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2MR B 501 DBREF 5VQH A 0 217 UNP H9JD76 TDRKH_BOMMO 245 462 DBREF 5VQH B 0 217 UNP H9JD76 TDRKH_BOMMO 245 462 SEQADV 5VQH MET A -19 UNP H9JD76 INITIATING METHIONINE SEQADV 5VQH GLY A -18 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH SER A -17 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH SER A -16 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH HIS A -15 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH HIS A -14 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH HIS A -13 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH HIS A -12 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH HIS A -11 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH HIS A -10 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH GLU A -9 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH ASN A -8 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH LEU A -7 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH TYR A -6 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH PHE A -5 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH GLN A -4 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH SER A -3 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH ASN A -2 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH ALA A -1 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH ARG A 144 UNP H9JD76 THR 389 CONFLICT SEQADV 5VQH MET B -19 UNP H9JD76 INITIATING METHIONINE SEQADV 5VQH GLY B -18 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH SER B -17 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH SER B -16 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH HIS B -15 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH HIS B -14 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH HIS B -13 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH HIS B -12 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH HIS B -11 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH HIS B -10 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH GLU B -9 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH ASN B -8 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH LEU B -7 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH TYR B -6 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH PHE B -5 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH GLN B -4 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH SER B -3 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH ASN B -2 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH ALA B -1 UNP H9JD76 EXPRESSION TAG SEQADV 5VQH ARG B 144 UNP H9JD76 THR 389 CONFLICT SEQRES 1 A 237 MET GLY SER SER HIS HIS HIS HIS HIS HIS GLU ASN LEU SEQRES 2 A 237 TYR PHE GLN SER ASN ALA GLY PRO SER ILE GLU VAL TYR SEQRES 3 A 237 VAL SER ALA VAL SER SER PRO SER ARG PHE TRP VAL GLN SEQRES 4 A 237 PHE VAL GLY PRO GLN VAL ALA GLN LEU ASP ASP LEU VAL SEQRES 5 A 237 ALA HIS MET THR GLU TYR TYR SER LYS LYS GLU ASN ARG SEQRES 6 A 237 GLU ALA HIS THR LEU ARG HIS VAL SER VAL GLY GLN VAL SEQRES 7 A 237 VAL ALA ALA VAL PHE ARG HIS ASP GLY ARG TRP TYR ARG SEQRES 8 A 237 ALA ARG VAL HIS ASP ILE ARG PRO ASN GLU PHE ASP SER SEQRES 9 A 237 SER GLN GLN VAL ALA ASP VAL PHE TYR LEU ASP TYR GLY SEQRES 10 A 237 ASP SER GLU TYR VAL ALA THR HIS GLU LEU CYS GLU LEU SEQRES 11 A 237 ARG ALA ASP LEU LEU ARG LEU ARG PHE GLN ALA MET GLU SEQRES 12 A 237 CYS PHE LEU ALA GLY VAL ARG PRO ALA SER GLY GLU GLU SEQRES 13 A 237 ALA VAL SER PRO SER GLY GLN ARG TRP ASP LYS TRP HIS SEQRES 14 A 237 PRO GLN ALA VAL GLU ARG PHE GLU GLU LEU THR GLN VAL SEQRES 15 A 237 ALA ARG TRP LYS ALA LEU VAL SER ARG THR CYS THR TYR SEQRES 16 A 237 LYS LYS THR ALA THR ALA GLU GLY GLU LYS ASP LYS GLU SEQRES 17 A 237 ILE PRO GLY ILE LYS LEU PHE ASP VAL THR ASP GLU GLY SEQRES 18 A 237 GLU LEU ASP VAL GLY ALA VAL LEU VAL ALA GLU GLY TRP SEQRES 19 A 237 ALA VAL ALA SEQRES 1 B 237 MET GLY SER SER HIS HIS HIS HIS HIS HIS GLU ASN LEU SEQRES 2 B 237 TYR PHE GLN SER ASN ALA GLY PRO SER ILE GLU VAL TYR SEQRES 3 B 237 VAL SER ALA VAL SER SER PRO SER ARG PHE TRP VAL GLN SEQRES 4 B 237 PHE VAL GLY PRO GLN VAL ALA GLN LEU ASP ASP LEU VAL SEQRES 5 B 237 ALA HIS MET THR GLU TYR TYR SER LYS LYS GLU ASN ARG SEQRES 6 B 237 GLU ALA HIS THR LEU ARG HIS VAL SER VAL GLY GLN VAL SEQRES 7 B 237 VAL ALA ALA VAL PHE ARG HIS ASP GLY ARG TRP TYR ARG SEQRES 8 B 237 ALA ARG VAL HIS ASP ILE ARG PRO ASN GLU PHE ASP SER SEQRES 9 B 237 SER GLN GLN VAL ALA ASP VAL PHE TYR LEU ASP TYR GLY SEQRES 10 B 237 ASP SER GLU TYR VAL ALA THR HIS GLU LEU CYS GLU LEU SEQRES 11 B 237 ARG ALA ASP LEU LEU ARG LEU ARG PHE GLN ALA MET GLU SEQRES 12 B 237 CYS PHE LEU ALA GLY VAL ARG PRO ALA SER GLY GLU GLU SEQRES 13 B 237 ALA VAL SER PRO SER GLY GLN ARG TRP ASP LYS TRP HIS SEQRES 14 B 237 PRO GLN ALA VAL GLU ARG PHE GLU GLU LEU THR GLN VAL SEQRES 15 B 237 ALA ARG TRP LYS ALA LEU VAL SER ARG THR CYS THR TYR SEQRES 16 B 237 LYS LYS THR ALA THR ALA GLU GLY GLU LYS ASP LYS GLU SEQRES 17 B 237 ILE PRO GLY ILE LYS LEU PHE ASP VAL THR ASP GLU GLY SEQRES 18 B 237 GLU LEU ASP VAL GLY ALA VAL LEU VAL ALA GLU GLY TRP SEQRES 19 B 237 ALA VAL ALA HET 2MR A 501 14 HET 2MR B 501 14 HETNAM 2MR N3, N4-DIMETHYLARGININE FORMUL 3 2MR 2(C8 H18 N4 O2) FORMUL 5 HOH *153(H2 O) HELIX 1 AA1 GLY A 22 SER A 40 1 19 HELIX 2 AA2 LYS A 41 ALA A 47 1 7 HELIX 3 AA3 HIS A 105 LEU A 107 5 3 HELIX 4 AA4 ARG A 111 ARG A 116 5 6 HELIX 5 AA5 HIS A 149 THR A 160 1 12 HELIX 6 AA6 VAL A 205 GLU A 212 1 8 HELIX 7 AA7 PRO B 23 LYS B 41 1 19 HELIX 8 AA8 LYS B 41 ALA B 47 1 7 HELIX 9 AA9 HIS B 105 LEU B 107 5 3 HELIX 10 AB1 ARG B 111 ARG B 116 5 6 HELIX 11 AB2 HIS B 149 GLN B 161 1 13 HELIX 12 AB3 VAL B 205 GLU B 212 1 8 SHEET 1 AA1 7 LEU A -7 PHE A -5 0 SHEET 2 AA1 7 ALA A 167 THR A 178 -1 O TYR A 175 N TYR A -6 SHEET 3 AA1 7 ILE A 3 SER A 12 -1 N ILE A 3 O SER A 170 SHEET 4 AA1 7 ARG A 15 PHE A 20 -1 O ARG A 15 N SER A 12 SHEET 5 AA1 7 MET A 122 LEU A 126 -1 O CYS A 124 N PHE A 16 SHEET 6 AA1 7 LYS A 187 VAL A 197 1 O ILE A 192 N PHE A 125 SHEET 7 AA1 7 GLU A 202 ASP A 204 -1 O LEU A 203 N ASP A 196 SHEET 1 AA2 4 LEU A -7 PHE A -5 0 SHEET 2 AA2 4 ALA A 167 THR A 178 -1 O TYR A 175 N TYR A -6 SHEET 3 AA2 4 LYS A 187 VAL A 197 -1 O LYS A 187 N THR A 178 SHEET 4 AA2 4 GLU A 202 ASP A 204 -1 O LEU A 203 N ASP A 196 SHEET 1 AA3 5 SER A 99 ALA A 103 0 SHEET 2 AA3 5 VAL A 88 TYR A 93 -1 N ALA A 89 O VAL A 102 SHEET 3 AA3 5 TRP A 69 ARG A 78 -1 N HIS A 75 O ASP A 90 SHEET 4 AA3 5 VAL A 58 VAL A 62 -1 N VAL A 59 O ALA A 72 SHEET 5 AA3 5 CYS A 108 GLU A 109 -1 O CYS A 108 N ALA A 60 SHEET 1 AA4 2 ARG A 130 PRO A 131 0 SHEET 2 AA4 2 ALA A 215 VAL A 216 -1 O VAL A 216 N ARG A 130 SHEET 1 AA5 7 GLU B 202 ASP B 204 0 SHEET 2 AA5 7 ILE B 189 VAL B 197 -1 N ASP B 196 O LEU B 203 SHEET 3 AA5 7 ALA B 167 LYS B 176 -1 N VAL B 169 O PHE B 195 SHEET 4 AA5 7 ILE B 3 SER B 12 -1 N VAL B 5 O LEU B 168 SHEET 5 AA5 7 ARG B 15 PHE B 20 -1 O TRP B 17 N ALA B 9 SHEET 6 AA5 7 MET B 122 LEU B 126 -1 O CYS B 124 N PHE B 16 SHEET 7 AA5 7 ILE B 189 VAL B 197 1 O ILE B 192 N PHE B 125 SHEET 1 AA6 5 SER B 99 ALA B 103 0 SHEET 2 AA6 5 GLN B 87 TYR B 93 -1 N VAL B 91 O GLU B 100 SHEET 3 AA6 5 TRP B 69 PRO B 79 -1 N ARG B 78 O VAL B 88 SHEET 4 AA6 5 VAL B 58 VAL B 62 -1 N VAL B 59 O ALA B 72 SHEET 5 AA6 5 CYS B 108 GLU B 109 -1 O CYS B 108 N ALA B 60 SHEET 1 AA7 2 ARG B 130 PRO B 131 0 SHEET 2 AA7 2 ALA B 215 VAL B 216 -1 O VAL B 216 N ARG B 130 SITE 1 AC1 6 ASP A 66 ARG A 68 TYR A 70 TYR A 93 SITE 2 AC1 6 TYR A 96 ASP A 98 SITE 1 AC2 10 ASN A 80 ASP A 83 SER B 8 PHE B 63 SITE 2 AC2 10 ARG B 68 TYR B 70 TYR B 93 TYR B 96 SITE 3 AC2 10 ASP B 98 TRP B 165 CRYST1 66.030 66.030 224.480 90.00 90.00 90.00 P 43 21 2 16 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 0.015145 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015145 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004455 0.00000