HEADER RNA BINDING PROTEIN/RNA 15-MAY-20 7C45 TITLE THE CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI RNASE D COMPLEX WITH RNA TITLE 2 U12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CCHC-TYPE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE D; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'); COMPND 8 CHAIN: D; COMPND 9 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; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS TRYPANOSOMA BRUCEI, RNASE D, GUIDE RNA DEGRADATION, RNA BINDING KEYWDS 2 PROTEIN, RNA U12, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.Q.GAO,J.H.GAN REVDAT 2 27-MAR-24 7C45 1 REMARK REVDAT 1 07-APR-21 7C45 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. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 26921 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1356 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 36.8400 - 3.8104 0.93 2754 157 0.1640 0.1793 REMARK 3 2 3.8104 - 3.0249 0.95 2710 136 0.1752 0.2053 REMARK 3 3 3.0249 - 2.6426 0.97 2693 162 0.2030 0.2334 REMARK 3 4 2.6426 - 2.4011 0.96 2699 117 0.2086 0.2313 REMARK 3 5 2.4011 - 2.2290 0.97 2676 131 0.2082 0.2469 REMARK 3 6 2.2290 - 2.0976 0.96 2655 138 0.2047 0.2180 REMARK 3 7 2.0976 - 1.9926 0.91 2480 138 0.2147 0.2748 REMARK 3 8 1.9926 - 1.9058 0.88 2427 142 0.2159 0.2634 REMARK 3 9 1.9058 - 1.8325 0.84 2321 112 0.2304 0.2975 REMARK 3 10 1.8325 - 1.7692 0.79 2150 123 0.2317 0.2817 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.26 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 : 0.008 2522 REMARK 3 ANGLE : 0.989 3458 REMARK 3 CHIRALITY : 0.056 410 REMARK 3 PLANARITY : 0.006 411 REMARK 3 DIHEDRAL : 19.289 1499 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): 15.5865 -5.6245 -11.4800 REMARK 3 T TENSOR REMARK 3 T11: 0.1661 T22: 0.1781 REMARK 3 T33: 0.1883 T12: 0.0014 REMARK 3 T13: 0.0153 T23: 0.0244 REMARK 3 L TENSOR REMARK 3 L11: 0.2102 L22: 0.5495 REMARK 3 L33: 0.8558 L12: 0.1470 REMARK 3 L13: 0.3261 L23: 0.4562 REMARK 3 S TENSOR REMARK 3 S11: 0.0364 S12: -0.0194 S13: -0.0332 REMARK 3 S21: 0.0222 S22: 0.0041 S23: -0.0598 REMARK 3 S31: 0.0185 S32: 0.0214 S33: -0.0438 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 7C45 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_1300016991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 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-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28011 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.769 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.47300 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 (%): 37.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE, 20% REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING 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 22.22450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.95700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.92150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.95700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.22450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.92150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 GLN A 196 REMARK 465 GLU A 197 REMARK 465 GLY A 198 REMARK 465 GLY A 209 REMARK 465 ASN A 210 REMARK 465 U D 13 REMARK 465 U D 14 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 MET A 49 CG SD CE REMARK 470 GLU A 66 CD OE1 OE2 REMARK 470 GLN A 89 CG CD OE1 NE2 REMARK 470 LYS A 124 CG CD CE NZ REMARK 470 ARG A 133 CD NE CZ NH1 NH2 REMARK 470 THR A 207 OG1 CG2 REMARK 470 ARG A 211 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 245 CG CD CE NZ REMARK 470 LYS A 317 CG CD CE NZ 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 OD1 ASN A 315 O HOH A 501 2.04 REMARK 500 OD1 ASP A 230 O HOH A 502 2.05 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 LEU A 129 CA - CB - CG ANGL. DEV. = 14.4 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 THR A 86 -149.40 -120.59 REMARK 500 THR A 118 143.86 80.68 REMARK 500 ASP A 141 94.62 61.06 REMARK 500 VAL A 213 -63.44 76.39 REMARK 500 ALA A 266 77.86 -106.16 REMARK 500 ALA A 280 33.22 -96.23 REMARK 500 ASN A 283 118.67 -38.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 704 DISTANCE = 6.22 ANGSTROMS 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 CA A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 80 OD1 REMARK 620 2 ASP A 80 OD2 43.5 REMARK 620 3 GLU A 82 OE2 92.2 92.9 REMARK 620 4 ASP A 230 OD2 101.2 90.9 164.0 REMARK 620 5 HOH A 606 O 128.0 84.6 94.4 70.5 REMARK 620 6 HOH A 666 O 164.5 152.0 87.0 82.4 67.5 REMARK 620 7 U D 12 OP1 71.2 113.6 101.3 91.4 155.0 93.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA D 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 80 OD1 REMARK 620 2 HOH A 513 O 80.6 REMARK 620 3 HOH A 515 O 103.4 81.7 REMARK 620 4 HOH A 619 O 103.0 157.1 75.5 REMARK 620 5 U D 11 O3' 144.6 96.7 111.1 93.1 REMARK 620 6 U D 12 OP1 82.8 98.5 173.7 104.3 62.5 REMARK 620 N 1 2 3 4 5 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 297 SG REMARK 620 2 CYS A 300 SG 110.5 REMARK 620 3 HIS A 305 NE2 99.9 104.3 REMARK 620 4 CYS A 310 SG 108.8 119.1 112.5 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 320 SG REMARK 620 2 CYS A 323 SG 111.6 REMARK 620 3 HIS A 328 NE2 99.2 102.8 REMARK 620 4 CYS A 333 SG 108.7 118.7 114.2 REMARK 620 N 1 2 3 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 CA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA D 101 DBREF 7C45 A 40 341 UNP Q38DE2 Q38DE2_TRYB2 40 341 DBREF 7C45 D 3 14 PDB 7C45 7C45 3 14 SEQRES 1 A 302 THR SER SER ALA THR SER SER SER SER MET ILE LEU LYS SEQRES 2 A 302 TYR PRO TYR ARG VAL VAL ASP THR HIS GLU LYS LEU LYS SEQRES 3 A 302 GLU ALA VAL THR SER LEU GLN GLY ALA ARG SER ILE ALA SEQRES 4 A 302 LEU ASP ILE GLU ALA PHE CYS THR THR ASP GLN ALA LYS SEQRES 5 A 302 GLN LEU GLY ARG ILE SER LEU VAL GLN ALA CYS SER ASP SEQRES 6 A 302 ALA LYS PRO VAL VAL PHE LEU PHE ASP VAL LEU THR LEU SEQRES 7 A 302 THR PRO ASP VAL PHE VAL LYS ASP MET GLN SER LEU LEU SEQRES 8 A 302 SER ASP ARG GLU ILE ARG LYS LEU PHE PHE ASP CYS ARG SEQRES 9 A 302 ARG ASP VAL GLU ALA LEU SER CYS GLN LEU GLY VAL LYS SEQRES 10 A 302 PRO GLU GLY VAL LEU ASP LEU GLN VAL PHE PHE THR ALA SEQRES 11 A 302 ILE GLN TRP LYS LEU ARG SER VAL ASN ARG ARG SER GLY SEQRES 12 A 302 MET GLY TYR VAL LEU LYS SER VAL ALA GLY LEU THR ARG SEQRES 13 A 302 GLN GLU GLY ASP SER ALA VAL GLN THR ALA MET THR LEU SEQRES 14 A 302 GLY ASN ARG PRO VAL TRP ASP ILE ARG PRO LEU PRO ASP SEQRES 15 A 302 HIS PHE LEU GLU TYR ALA ALA GLY ASP VAL ARG HIS ILE SEQRES 16 A 302 LEU LEU LEU SER ASN TYR LEU VAL GLY ASN LYS ASP VAL SEQRES 17 A 302 PRO VAL ASP VAL VAL ALA VAL GLU ARG LEU THR ALA GLN SEQRES 18 A 302 TYR VAL GLU HIS TYR ALA VAL GLY LYS PRO VAL ILE THR SEQRES 19 A 302 GLU ALA ASP ALA THR PRO ALA GLU VAL ASN ARG ALA TRP SEQRES 20 A 302 LEU GLU ARG TYR ILE GLY PRO GLY GLY GLY CYS HIS PHE SEQRES 21 A 302 CYS GLY ALA LYS GLY HIS THR GLU ALA GLU CYS PHE LYS SEQRES 22 A 302 LYS GLN ASN GLY LYS ALA LYS CYS SER PHE CYS GLY GLU SEQRES 23 A 302 VAL GLY HIS THR ALA ARG ASN CYS PHE LYS LYS HIS PRO SEQRES 24 A 302 GLN LEU LEU SEQRES 1 D 12 U U U U U U U U U U U U HET ZN A 401 1 HET ZN A 402 1 HET CA A 403 1 HET CA D 101 1 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION FORMUL 3 ZN 2(ZN 2+) FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *225(H2 O) HELIX 1 AA1 SER A 42 LYS A 52 1 11 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 ASP A 132 1 15 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 SER A 200 LEU A 208 1 9 HELIX 9 AA9 PRO A 220 VAL A 242 1 23 HELIX 10 AB1 ASP A 250 ALA A 266 1 17 HELIX 11 AB2 ASN A 283 ILE A 291 1 9 HELIX 12 AB3 THR A 306 GLU A 309 5 4 HELIX 13 AB4 CYS A 310 ASN A 315 1 6 HELIX 14 AB5 THR A 329 CYS A 333 5 5 HELIX 15 AB6 HIS A 337 LEU A 341 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 VAL A 99 O PHE A 112 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 OD1 ASP A 80 CA CA A 403 1555 1555 3.15 LINK OD2 ASP A 80 CA CA A 403 1555 1555 2.20 LINK OD1 ASP A 80 CA CA D 101 1555 1555 2.40 LINK OE2 GLU A 82 CA CA A 403 1555 1555 2.29 LINK OD2 ASP A 230 CA CA A 403 1555 1555 2.42 LINK SG CYS A 297 ZN ZN A 401 1555 1555 2.33 LINK SG CYS A 300 ZN ZN A 401 1555 1555 2.36 LINK NE2 HIS A 305 ZN ZN A 401 1555 1555 2.16 LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.34 LINK SG CYS A 320 ZN ZN A 402 1555 1555 2.41 LINK SG CYS A 323 ZN ZN A 402 1555 1555 2.29 LINK NE2 HIS A 328 ZN ZN A 402 1555 1555 2.06 LINK SG CYS A 333 ZN ZN A 402 1555 1555 2.34 LINK CA CA A 403 O HOH A 606 1555 1555 2.87 LINK CA CA A 403 O HOH A 666 1555 1555 2.49 LINK CA CA A 403 OP1 U D 12 1555 1555 2.23 LINK O HOH A 513 CA CA D 101 1555 1555 2.38 LINK O HOH A 515 CA CA D 101 1555 1555 2.48 LINK O HOH A 619 CA CA D 101 1555 1555 2.44 LINK O3' U D 11 CA CA D 101 1555 1555 2.22 LINK OP1 U D 12 CA CA D 101 1555 1555 2.46 CISPEP 1 ARG A 217 PRO A 218 0 -4.55 SITE 1 AC1 4 CYS A 297 CYS A 300 HIS A 305 CYS A 310 SITE 1 AC2 4 CYS A 320 CYS A 323 HIS A 328 CYS A 333 SITE 1 AC3 6 ASP A 80 GLU A 82 ASP A 230 HOH A 606 SITE 2 AC3 6 HOH A 666 U D 12 SITE 1 AC4 6 ASP A 80 HOH A 513 HOH A 515 HOH A 619 SITE 2 AC4 6 U D 11 U D 12 CRYST1 44.449 65.843 99.914 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 0.022498 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015188 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010009 0.00000