HEADER RNA BINDING PROTEIN 15-MAY-20 7C4C TITLE THE CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI RNASE D : GMP COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CCHC-TYPE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI BRUCEI (STRAIN 927/4 SOURCE 3 GUTAT10.1); SOURCE 4 ORGANISM_TAXID: 185431; SOURCE 5 STRAIN: 927/4 GUTAT10.1; SOURCE 6 GENE: TB09.211.3670; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRYPANOSOMA BRUCEI, RNASE D, GUIDE RNA DEGRADATION, RNA BINDING KEYWDS 2 PROTEIN, GMP EXPDTA X-RAY DIFFRACTION AUTHOR Y.Q.GAO,J.H.GAN REVDAT 1 07-APR-21 7C4C 0 JRNL AUTH Y.GAO,H.LIU,C.ZHANG,S.SU,Y.CHEN,X.CHEN,Y.LI,Z.SHAO,Y.ZHANG, JRNL AUTH 2 Q.SHAO,J.LI,Z.HUANG,J.MA,J.GAN JRNL TITL STRUCTURAL BASIS FOR GUIDE RNA TRIMMING BY RNASE D JRNL TITL 2 RIBONUCLEASE IN TRYPANOSOMA BRUCEI. JRNL REF NUCLEIC ACIDS RES. V. 49 568 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 33332555 JRNL DOI 10.1093/NAR/GKAA1197 REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 17979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 918 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.0000 - 4.3289 0.99 2980 154 0.1629 0.2265 REMARK 3 2 4.3289 - 3.4376 1.00 2854 148 0.1624 0.2016 REMARK 3 3 3.4376 - 3.0035 1.00 2793 160 0.2019 0.2361 REMARK 3 4 3.0035 - 2.7291 0.99 2761 170 0.2262 0.2562 REMARK 3 5 2.7291 - 2.5336 0.94 2639 140 0.2433 0.2860 REMARK 3 6 2.5336 - 2.3843 0.73 2029 106 0.2477 0.3197 REMARK 3 7 2.3843 - 2.2650 0.36 1005 40 0.2385 0.2508 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 2662 REMARK 3 ANGLE : 0.940 3618 REMARK 3 CHIRALITY : 0.051 404 REMARK 3 PLANARITY : 0.007 456 REMARK 3 DIHEDRAL : 16.683 1563 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -17.2869 8.6059 -12.4793 REMARK 3 T TENSOR REMARK 3 T11: 0.1580 T22: 0.1879 REMARK 3 T33: 0.2095 T12: 0.0032 REMARK 3 T13: -0.0240 T23: 0.0169 REMARK 3 L TENSOR REMARK 3 L11: 0.5301 L22: 0.4594 REMARK 3 L33: 1.2156 L12: 0.4498 REMARK 3 L13: -0.6854 L23: -0.2730 REMARK 3 S TENSOR REMARK 3 S11: -0.0420 S12: 0.0334 S13: 0.2182 REMARK 3 S21: -0.0880 S22: 0.0781 S23: 0.0589 REMARK 3 S31: 0.0208 S32: -0.0380 S33: -0.0470 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7C4C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1300016999. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20606 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 30.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.40500 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: HKL2MAP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 30% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 28.58450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.70450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.50050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.70450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.58450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.50050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL 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 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 THR A 40 REMARK 465 SER A 41 REMARK 465 SER A 42 REMARK 465 ALA A 43 REMARK 465 THR A 44 REMARK 465 SER A 45 REMARK 465 SER A 46 REMARK 465 TRP A 379 REMARK 465 GLN A 380 REMARK 465 GLN A 381 REMARK 465 LYS A 382 REMARK 465 ARG A 383 REMARK 465 LEU A 384 REMARK 465 GLY A 385 REMARK 465 GLU A 386 REMARK 465 ASN A 387 REMARK 465 SER A 388 REMARK 465 LEU A 389 REMARK 465 HIS A 390 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 SER A 47 CB OG REMARK 470 ASP A 88 CG OD1 OD2 REMARK 470 GLN A 89 CB CG CD OE1 NE2 REMARK 470 ARG A 331 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 344 CG CD OE1 OE2 REMARK 470 LYS A 345 CG CD CE NZ REMARK 470 GLN A 348 CG CD OE1 NE2 REMARK 470 THR A 354 OG1 CG2 REMARK 470 ARG A 358 CG CD NE CZ NH1 NH2 REMARK 470 THR A 359 OG1 CG2 REMARK 470 ASN A 360 CG OD1 ND2 REMARK 470 ILE A 378 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 OD2 ASP A 145 O HOH A 501 2.11 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 PRO A 368 C - N - CD ANGL. DEV. = -12.9 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 THR A 118 151.56 89.37 REMARK 500 ASP A 141 98.98 57.96 REMARK 500 ARG A 175 -0.40 -140.61 REMARK 500 VAL A 213 -61.31 76.28 REMARK 500 ALA A 280 31.99 -98.79 REMARK 500 ASN A 283 114.32 -38.53 REMARK 500 CYS A 346 -21.96 -141.86 REMARK 500 THR A 354 9.20 -67.61 REMARK 500 SER A 355 58.25 -158.63 REMARK 500 HIS A 369 -175.99 -175.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 5GP A 414 REMARK 610 5GP A 416 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 61 NE2 REMARK 620 2 LYS A 65 NZ 78.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 407 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 80 OD2 REMARK 620 2 GLU A 82 OE1 106.0 REMARK 620 3 ASP A 230 OD2 94.1 128.3 REMARK 620 4 5GP A 413 O2P 83.5 121.2 107.8 REMARK 620 5 HOH A 521 O 168.4 76.4 93.1 85.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 408 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 80 OD1 REMARK 620 2 5GP A 413 O2P 94.2 REMARK 620 3 5GP A 413 O3P 158.0 63.9 REMARK 620 4 HOH A 501 O 90.5 173.9 111.5 REMARK 620 5 HOH A 503 O 94.5 88.5 87.5 87.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 197 OE2 REMARK 620 2 HIS A 233 NE2 99.8 REMARK 620 3 HIS A 375 NE2 114.2 95.8 REMARK 620 4 HOH A 539 O 113.3 117.3 114.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 297 SG REMARK 620 2 CYS A 300 SG 102.3 REMARK 620 3 HIS A 305 NE2 103.4 107.0 REMARK 620 4 CYS A 310 SG 113.6 120.7 108.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 320 SG REMARK 620 2 CYS A 323 SG 106.6 REMARK 620 3 HIS A 328 NE2 102.0 94.1 REMARK 620 4 CYS A 333 SG 113.5 116.5 121.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 409 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 325 OE1 REMARK 620 2 GLU A 325 OE2 52.1 REMARK 620 3 5GP A 414 N7 79.8 131.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 406 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 343 SG REMARK 620 2 CYS A 346 SG 88.2 REMARK 620 3 CYS A 356 SG 148.3 114.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 405 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 362 SG REMARK 620 2 CYS A 365 SG 110.5 REMARK 620 3 CYS A 374 SG 107.5 122.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5GP A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5GP A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5GP A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5GP A 416 DBREF 7C4C A 40 390 UNP Q38DE2 Q38DE2_TRYB2 40 390 SEQRES 1 A 351 THR SER SER ALA THR SER SER SER SER MSE ILE LEU LYS SEQRES 2 A 351 TYR PRO TYR ARG VAL VAL ASP THR HIS GLU LYS LEU LYS SEQRES 3 A 351 GLU ALA VAL THR SER LEU GLN GLY ALA ARG SER ILE ALA SEQRES 4 A 351 LEU ASP ILE GLU ALA PHE CYS THR THR ASP GLN ALA LYS SEQRES 5 A 351 GLN LEU GLY ARG ILE SER LEU VAL GLN ALA CYS SER ASP SEQRES 6 A 351 ALA LYS PRO VAL VAL PHE LEU PHE ASP VAL LEU THR LEU SEQRES 7 A 351 THR PRO ASP VAL PHE VAL LYS ASP MSE GLN SER LEU LEU SEQRES 8 A 351 SER ASP ARG GLU ILE ARG LYS LEU PHE PHE ASP CYS ARG SEQRES 9 A 351 ARG ASP VAL GLU ALA LEU SER CYS GLN LEU GLY VAL LYS SEQRES 10 A 351 PRO GLU GLY VAL LEU ASP LEU GLN VAL PHE PHE THR ALA SEQRES 11 A 351 ILE GLN TRP LYS LEU ARG SER VAL ASN ARG ARG SER GLY SEQRES 12 A 351 MSE GLY TYR VAL LEU LYS SER VAL ALA GLY LEU THR ARG SEQRES 13 A 351 GLN GLU GLY ASP SER ALA VAL GLN THR ALA MSE THR LEU SEQRES 14 A 351 GLY ASN ARG PRO VAL TRP ASP ILE ARG PRO LEU PRO ASP SEQRES 15 A 351 HIS PHE LEU GLU TYR ALA ALA GLY ASP VAL ARG HIS ILE SEQRES 16 A 351 LEU LEU LEU SER ASN TYR LEU VAL GLY ASN LYS ASP VAL SEQRES 17 A 351 PRO VAL ASP VAL VAL ALA VAL GLU ARG LEU THR ALA GLN SEQRES 18 A 351 TYR VAL GLU HIS TYR ALA VAL GLY LYS PRO VAL ILE THR SEQRES 19 A 351 GLU ALA ASP ALA THR PRO ALA GLU VAL ASN ARG ALA TRP SEQRES 20 A 351 LEU GLU ARG TYR ILE GLY PRO GLY GLY GLY CYS HIS PHE SEQRES 21 A 351 CYS GLY ALA LYS GLY HIS THR GLU ALA GLU CYS PHE LYS SEQRES 22 A 351 LYS GLN ASN GLY LYS ALA LYS CYS SER PHE CYS GLY GLU SEQRES 23 A 351 VAL GLY HIS THR ALA ARG ASN CYS PHE LYS LYS HIS PRO SEQRES 24 A 351 GLN LEU LEU THR CYS GLU LYS CYS GLY GLN LEU GLY HIS SEQRES 25 A 351 THR GLY THR SER CYS PHE ARG THR ASN PRO CYS LYS HIS SEQRES 26 A 351 CYS GLY GLY PRO HIS SER SER ALA ASN CYS HIS LYS VAL SEQRES 27 A 351 ILE TRP GLN GLN LYS ARG LEU GLY GLU ASN SER LEU HIS MODRES 7C4C MSE A 49 MET MODIFIED RESIDUE MODRES 7C4C MSE A 126 MET MODIFIED RESIDUE MODRES 7C4C MSE A 183 MET MODIFIED RESIDUE MODRES 7C4C MSE A 206 MET MODIFIED RESIDUE HET MSE A 49 8 HET MSE A 126 8 HET MSE A 183 8 HET MSE A 206 8 HET ZN A 401 1 HET ZN A 402 1 HET ZN A 403 1 HET ZN A 404 1 HET ZN A 405 1 HET ZN A 406 1 HET MN A 407 1 HET MN A 408 1 HET MN A 409 1 HET MN A 410 1 HET MN A 411 1 HET MN A 412 1 HET 5GP A 413 24 HET 5GP A 414 18 HET 5GP A 415 24 HET 5GP A 416 12 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 ZN 6(ZN 2+) FORMUL 8 MN 6(MN 2+) FORMUL 14 5GP 4(C10 H14 N5 O8 P) FORMUL 18 HOH *41(H2 O) HELIX 1 AA1 MSE A 49 TYR A 53 5 5 HELIX 2 AA2 THR A 60 GLY A 73 1 14 HELIX 3 AA3 VAL A 114 THR A 118 1 5 HELIX 4 AA4 THR A 118 SER A 131 1 14 HELIX 5 AA5 CYS A 142 GLY A 154 1 13 HELIX 6 AA6 LEU A 163 SER A 176 1 14 HELIX 7 AA7 GLY A 182 GLY A 192 1 11 HELIX 8 AA8 ARG A 195 ASP A 199 5 5 HELIX 9 AA9 SER A 200 GLY A 209 1 10 HELIX 10 AB1 PRO A 220 VAL A 242 1 23 HELIX 11 AB2 ASP A 250 ALA A 266 1 17 HELIX 12 AB3 ASN A 283 ILE A 291 1 9 HELIX 13 AB4 THR A 306 GLU A 309 5 4 HELIX 14 AB5 CYS A 310 GLY A 316 1 7 HELIX 15 AB6 THR A 329 CYS A 333 5 5 HELIX 16 AB7 HIS A 337 LEU A 341 5 5 HELIX 17 AB8 THR A 352 CYS A 356 5 5 SHEET 1 AA1 6 TYR A 55 VAL A 58 0 SHEET 2 AA1 6 VAL A 109 ASP A 113 1 O LEU A 111 N VAL A 58 SHEET 3 AA1 6 ILE A 96 SER A 103 -1 N ALA A 101 O PHE A 110 SHEET 4 AA1 6 SER A 76 ALA A 83 -1 N ALA A 78 O CYS A 102 SHEET 5 AA1 6 ARG A 136 PHE A 139 1 O LEU A 138 N LEU A 79 SHEET 6 AA1 6 VAL A 160 ASP A 162 1 O LEU A 161 N LYS A 137 LINK C SER A 48 N MSE A 49 1555 1555 1.33 LINK C MSE A 49 N ILE A 50 1555 1555 1.34 LINK C ASP A 125 N MSE A 126 1555 1555 1.33 LINK C MSE A 126 N GLN A 127 1555 1555 1.34 LINK C GLY A 182 N MSE A 183 1555 1555 1.33 LINK C MSE A 183 N GLY A 184 1555 1555 1.34 LINK C ALA A 205 N MSE A 206 1555 1555 1.34 LINK C MSE A 206 N THR A 207 1555 1555 1.34 LINK NE2 HIS A 61 ZN ZN A 403 1555 1555 2.35 LINK NZ LYS A 65 ZN ZN A 403 1555 1555 1.95 LINK OD2 ASP A 80 MN MN A 407 1555 1555 2.21 LINK OD1 ASP A 80 MN MN A 408 1555 1555 2.08 LINK OE1 GLU A 82 MN MN A 407 1555 1555 2.13 LINK OE2 GLU A 197 ZN ZN A 404 1555 1555 2.16 LINK OD2 ASP A 230 MN MN A 407 1555 1555 2.21 LINK NE2 HIS A 233 ZN ZN A 404 1555 1555 2.26 LINK SG CYS A 297 ZN ZN A 402 1555 1555 2.31 LINK SG CYS A 300 ZN ZN A 402 1555 1555 2.23 LINK NE2 HIS A 305 ZN ZN A 402 1555 1555 2.10 LINK SG CYS A 310 ZN ZN A 402 1555 1555 2.30 LINK SG CYS A 320 ZN ZN A 401 1555 1555 2.23 LINK SG CYS A 323 ZN ZN A 401 1555 1555 2.26 LINK OE1 GLU A 325 MN MN A 409 1555 1555 2.08 LINK OE2 GLU A 325 MN MN A 409 1555 1555 2.75 LINK NE2 HIS A 328 ZN ZN A 401 1555 1555 2.19 LINK SG CYS A 333 ZN ZN A 401 1555 1555 2.21 LINK SG CYS A 343 ZN ZN A 406 1555 1555 2.29 LINK SG CYS A 346 ZN ZN A 406 1555 1555 2.65 LINK SG CYS A 356 ZN ZN A 406 1555 1555 2.29 LINK SG CYS A 362 ZN ZN A 405 1555 1555 2.70 LINK SG CYS A 365 ZN ZN A 405 1555 1555 2.49 LINK SG CYS A 374 ZN ZN A 405 1555 1555 2.29 LINK NE2 HIS A 375 ZN ZN A 404 1555 2464 2.39 LINK ZN ZN A 404 O HOH A 539 1555 1555 2.35 LINK MN MN A 407 O2P 5GP A 413 1555 1555 2.09 LINK MN MN A 407 O HOH A 521 1555 1555 2.69 LINK MN MN A 408 O2P 5GP A 413 1555 1555 2.21 LINK MN MN A 408 O3P 5GP A 413 1555 1555 2.54 LINK MN MN A 408 O HOH A 501 1555 1555 2.10 LINK MN MN A 408 O HOH A 503 1555 1555 2.24 LINK MN MN A 409 N7 5GP A 414 1555 1555 2.25 LINK MN MN A 410 N7 5GP A 413 1555 1555 2.72 CISPEP 1 ARG A 217 PRO A 218 0 5.51 SITE 1 AC1 4 CYS A 320 CYS A 323 HIS A 328 CYS A 333 SITE 1 AC2 4 CYS A 297 CYS A 300 HIS A 305 CYS A 310 SITE 1 AC3 3 HIS A 61 LYS A 65 ASP A 125 SITE 1 AC4 4 GLU A 197 HIS A 233 HIS A 375 HOH A 539 SITE 1 AC5 4 CYS A 362 CYS A 365 HIS A 369 CYS A 374 SITE 1 AC6 4 CYS A 343 CYS A 346 HIS A 351 CYS A 356 SITE 1 AC7 5 ASP A 80 GLU A 82 ASP A 230 5GP A 413 SITE 2 AC7 5 HOH A 521 SITE 1 AC8 5 ASP A 80 ASP A 145 5GP A 413 HOH A 501 SITE 2 AC8 5 HOH A 503 SITE 1 AC9 3 GLU A 325 LYS A 335 5GP A 414 SITE 1 AD1 2 GLN A 203 5GP A 413 SITE 1 AD2 3 ALA A 330 LYS A 336 HIS A 337 SITE 1 AD3 1 5GP A 416 SITE 1 AD4 13 ASP A 80 ILE A 81 GLU A 82 ALA A 83 SITE 2 AD4 13 LEU A 93 MSE A 206 TRP A 214 ASP A 230 SITE 3 AD4 13 MN A 407 MN A 408 MN A 410 HOH A 512 SITE 4 AD4 13 HOH A 521 SITE 1 AD5 6 GLU A 325 HIS A 328 ASN A 332 CYS A 333 SITE 2 AD5 6 PHE A 334 MN A 409 SITE 1 AD6 3 ASP A 141 ARG A 143 GLN A 164 SITE 1 AD7 5 HIS A 305 GLU A 309 CYS A 310 PHE A 311 SITE 2 AD7 5 MN A 412 CRYST1 57.169 75.001 101.409 90.00 90.00 90.00 P 21 21 21 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 0.017492 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009861 0.00000