HEADER LYASE 12-AUG-20 7A1F TITLE CRYSTAL STRUCTURE OF HUMAN 5' EXONUCLEASE APPOLLO IN COMPLEX WITH TITLE 2 5'DAMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5' EXONUCLEASE APOLLO; COMPND 3 CHAIN: A, L; COMPND 4 SYNONYM: DNA CROSS-LINK REPAIR 1B PROTEIN,SNM1 HOMOLOG B,HSNM1B; COMPND 5 EC: 3.1.-.-; COMPND 6 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: DCLRE1B, SNM1B; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS DCLRE1B, SNM1B, EXONUCLEASE, APOLLO, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.NEWMAN,H.T.BADDOCK,S.M.M.MUKHOPADHYAY,N.A.BURGESS-BROWN,F.VON AUTHOR 2 DELFT,C.H.ARROWSHMITH,A.EDWARDS,C.BOUNTRA,O.GILEADI REVDAT 3 31-JAN-24 7A1F 1 REMARK REVDAT 2 03-AUG-22 7A1F 1 JRNL REVDAT 1 20-JAN-21 7A1F 0 JRNL AUTH H.T.BADDOCK,J.A.NEWMAN,Y.YOSAATMADJA,M.BIELINSKI, JRNL AUTH 2 C.J.SCHOFIELD,O.GILEADI,P.J.MCHUGH JRNL TITL A PHOSPHATE BINDING POCKET IS A KEY DETERMINANT OF EXO- JRNL TITL 2 VERSUS ENDO-NUCLEOLYTIC ACTIVITY IN THE SNM1 NUCLEASE JRNL TITL 3 FAMILY. JRNL REF NUCLEIC ACIDS RES. V. 49 9294 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 34387694 JRNL DOI 10.1093/NAR/GKAB692 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 55682 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2823 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 43.9530 - 4.8838 0.98 2752 178 0.1390 0.1605 REMARK 3 2 4.8838 - 3.8772 0.98 2795 126 0.1277 0.1387 REMARK 3 3 3.8772 - 3.3873 0.98 2825 125 0.1486 0.2091 REMARK 3 4 3.3873 - 3.0777 0.98 2785 159 0.1757 0.2343 REMARK 3 5 3.0777 - 2.8571 0.98 2730 181 0.1793 0.2083 REMARK 3 6 2.8571 - 2.6887 0.98 2787 165 0.1847 0.2190 REMARK 3 7 2.6887 - 2.5541 0.98 2770 157 0.1849 0.2448 REMARK 3 8 2.5541 - 2.4429 0.98 2759 151 0.1885 0.2491 REMARK 3 9 2.4429 - 2.3489 0.97 2745 133 0.1914 0.2502 REMARK 3 10 2.3489 - 2.2678 0.97 2763 114 0.1889 0.2757 REMARK 3 11 2.2678 - 2.1969 0.79 2215 137 0.1937 0.2635 REMARK 3 12 2.1969 - 2.1341 0.97 2744 180 0.1967 0.2714 REMARK 3 13 2.1341 - 2.0779 0.97 2713 142 0.2119 0.2656 REMARK 3 14 2.0779 - 2.0272 0.73 2081 109 0.2381 0.3066 REMARK 3 15 2.0272 - 1.9811 0.96 2749 120 0.2297 0.3276 REMARK 3 16 1.9811 - 1.9390 0.96 2694 142 0.2444 0.3106 REMARK 3 17 1.9390 - 1.9002 0.63 1827 75 0.2634 0.2881 REMARK 3 18 1.9002 - 1.8643 0.96 2689 148 0.2761 0.3140 REMARK 3 19 1.8643 - 1.8310 0.95 2730 142 0.2886 0.3257 REMARK 3 20 1.8310 - 1.8000 0.96 2706 139 0.3262 0.3958 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.97 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 : 0.007 5488 REMARK 3 ANGLE : 0.903 7495 REMARK 3 CHIRALITY : 0.055 854 REMARK 3 PLANARITY : 0.006 938 REMARK 3 DIHEDRAL : 13.357 3223 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7A1F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1292110706. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-17 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.31 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55714 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 68.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.62200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5AHO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M AMMONIUM CHLORIDE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 4320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, L 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 SER A 330 REMARK 465 SER A 331 REMARK 465 ARG A 332 REMARK 465 LYS A 333 REMARK 465 PRO A 334 REMARK 465 SER A 335 REMARK 465 ALA A 336 REMARK 465 GLU A 337 REMARK 465 ASN A 338 REMARK 465 LEU A 339 REMARK 465 TYR A 340 REMARK 465 PHE A 341 REMARK 465 GLN A 342 REMARK 465 ALA L 336 REMARK 465 GLU L 337 REMARK 465 ASN L 338 REMARK 465 LEU L 339 REMARK 465 TYR L 340 REMARK 465 PHE L 341 REMARK 465 GLN L 342 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 ARG A 300 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 313 CG CD NE CZ NH1 NH2 REMARK 470 ARG L 300 CG CD NE CZ NH1 NH2 REMARK 470 ARG L 313 CG CD NE CZ NH1 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 H3' D5M L 403 O2P D5M L 404 1.58 REMARK 500 OE1 GLU L 209 O HOH L 501 1.98 REMARK 500 O HOH A 593 O HOH L 776 2.05 REMARK 500 OG SER A 264 OD2 ASP L 321 2.09 REMARK 500 O HOH A 647 O HOH A 729 2.10 REMARK 500 O HOH A 513 O HOH A 723 2.12 REMARK 500 O HOH A 718 O HOH A 723 2.13 REMARK 500 O ARG L 20 O HOH L 502 2.16 REMARK 500 O HOH L 654 O HOH L 772 2.19 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 O HOH L 615 O HOH L 763 1465 2.14 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 AME A 1 O - C - N ANGL. DEV. = -13.4 DEGREES REMARK 500 AME L 1 O - C - N ANGL. DEV. = -11.1 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 ASN A 2 54.05 -105.10 REMARK 500 ALA A 21 55.38 -108.03 REMARK 500 ALA A 45 43.73 -144.30 REMARK 500 GLN A 87 -74.80 -108.02 REMARK 500 ASN L 2 55.34 -99.96 REMARK 500 ALA L 21 58.58 -102.87 REMARK 500 LYS L 225 15.95 58.01 REMARK 500 HIS L 249 139.65 -170.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 AME A 1 23.37 REMARK 500 AME L 1 22.76 REMARK 500 REMARK 500 REMARK: NULL 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 NI A 402 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 31 NE2 REMARK 620 2 HIS A 33 ND1 87.1 REMARK 620 3 HIS A 99 NE2 94.2 95.1 REMARK 620 4 ASP A 120 OD2 87.5 170.0 93.6 REMARK 620 5 D5M A 404 O2P 176.5 92.0 82.5 93.9 REMARK 620 6 HOH A 547 O 88.0 94.0 170.7 77.4 95.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 35 OD2 REMARK 620 2 HIS A 36 NE2 84.5 REMARK 620 3 ASP A 120 OD2 167.9 85.3 REMARK 620 4 D5M A 404 O3P 95.8 175.5 93.9 REMARK 620 5 HOH A 547 O 99.2 88.5 74.1 87.0 REMARK 620 6 HOH A 548 O 94.6 88.4 91.6 96.0 165.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI L 402 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS L 31 NE2 REMARK 620 2 HIS L 33 ND1 90.6 REMARK 620 3 HIS L 99 NE2 95.2 95.9 REMARK 620 4 ASP L 120 OD2 89.7 172.2 91.9 REMARK 620 5 D5M L 404 O3P 173.2 96.1 83.1 83.7 REMARK 620 6 HOH L 557 O 93.8 98.4 163.0 73.7 86.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE L 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP L 35 OD2 REMARK 620 2 HIS L 36 NE2 85.2 REMARK 620 3 ASP L 120 OD2 173.2 94.0 REMARK 620 4 D5M L 404 O1P 94.5 174.4 85.6 REMARK 620 5 HOH L 557 O 94.2 95.4 79.1 79.0 REMARK 620 6 HOH L 559 O 91.3 87.3 95.5 98.3 174.1 REMARK 620 N 1 2 3 4 5 DBREF 7A1F A 1 335 UNP Q9H816 DCR1B_HUMAN 1 335 DBREF 7A1F L 1 335 UNP Q9H816 DCR1B_HUMAN 1 335 SEQADV 7A1F ALA A 336 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F GLU A 337 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F ASN A 338 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F LEU A 339 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F TYR A 340 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F PHE A 341 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F GLN A 342 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F ALA L 336 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F GLU L 337 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F ASN L 338 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F LEU L 339 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F TYR L 340 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F PHE L 341 UNP Q9H816 EXPRESSION TAG SEQADV 7A1F GLN L 342 UNP Q9H816 EXPRESSION TAG SEQRES 1 A 342 AME ASN GLY VAL LEU ILE PRO HIS THR PRO ILE ALA VAL SEQRES 2 A 342 ASP PHE TRP SER LEU ARG ARG ALA GLY THR ALA ARG LEU SEQRES 3 A 342 PHE PHE LEU SER HIS MET HIS SER ASP HIS THR VAL GLY SEQRES 4 A 342 LEU SER SER THR TRP ALA ARG PRO LEU TYR CYS SER PRO SEQRES 5 A 342 ILE THR ALA HIS LEU LEU HIS ARG HIS LEU GLN VAL SER SEQRES 6 A 342 LYS GLN TRP ILE GLN ALA LEU GLU VAL GLY GLU SER HIS SEQRES 7 A 342 VAL LEU PRO LEU ASP GLU ILE GLY GLN GLU THR MET THR SEQRES 8 A 342 VAL THR LEU LEU ASP ALA ASN HIS CYS PRO GLY SER VAL SEQRES 9 A 342 MET PHE LEU PHE GLU GLY TYR PHE GLY THR ILE LEU TYR SEQRES 10 A 342 THR GLY ASP PHE ARG TYR THR PRO SER MET LEU LYS GLU SEQRES 11 A 342 PRO ALA LEU THR LEU GLY LYS GLN ILE HIS THR LEU TYR SEQRES 12 A 342 LEU ASP ASN THR ASN CYS ASN PRO ALA LEU VAL LEU PRO SEQRES 13 A 342 SER ARG GLN GLU ALA ALA HIS GLN ILE VAL GLN LEU ILE SEQRES 14 A 342 ARG LYS HIS PRO GLN HIS ASN ILE LYS ILE GLY LEU TYR SEQRES 15 A 342 SER LEU GLY LYS GLU SER LEU LEU GLU GLN LEU ALA LEU SEQRES 16 A 342 GLU PHE GLN THR TRP VAL VAL LEU SER PRO ARG ARG LEU SEQRES 17 A 342 GLU LEU VAL GLN LEU LEU GLY LEU ALA ASP VAL PHE THR SEQRES 18 A 342 VAL GLU GLU LYS ALA GLY ARG ILE HIS ALA VAL ASP HIS SEQRES 19 A 342 MET GLU ILE CYS HIS SER ASN MET LEU ARG TRP ASN GLN SEQRES 20 A 342 THR HIS PRO THR ILE ALA ILE LEU PRO THR SER ARG LYS SEQRES 21 A 342 ILE HIS SER SER HIS PRO ASP ILE HIS VAL ILE PRO TYR SEQRES 22 A 342 SER ASP HIS SER SER TYR SER GLU LEU ARG ALA PHE VAL SEQRES 23 A 342 ALA ALA LEU LYS PRO CYS GLN VAL VAL PRO ILE VAL SER SEQRES 24 A 342 ARG ARG PRO CYS GLY GLY PHE GLN ASP SER LEU SER PRO SEQRES 25 A 342 ARG ILE SER VAL PRO LEU ILE PRO ASP SER VAL GLN GLN SEQRES 26 A 342 TYR MET SER SER SER SER ARG LYS PRO SER ALA GLU ASN SEQRES 27 A 342 LEU TYR PHE GLN SEQRES 1 L 342 AME ASN GLY VAL LEU ILE PRO HIS THR PRO ILE ALA VAL SEQRES 2 L 342 ASP PHE TRP SER LEU ARG ARG ALA GLY THR ALA ARG LEU SEQRES 3 L 342 PHE PHE LEU SER HIS MET HIS SER ASP HIS THR VAL GLY SEQRES 4 L 342 LEU SER SER THR TRP ALA ARG PRO LEU TYR CYS SER PRO SEQRES 5 L 342 ILE THR ALA HIS LEU LEU HIS ARG HIS LEU GLN VAL SER SEQRES 6 L 342 LYS GLN TRP ILE GLN ALA LEU GLU VAL GLY GLU SER HIS SEQRES 7 L 342 VAL LEU PRO LEU ASP GLU ILE GLY GLN GLU THR MET THR SEQRES 8 L 342 VAL THR LEU LEU ASP ALA ASN HIS CYS PRO GLY SER VAL SEQRES 9 L 342 MET PHE LEU PHE GLU GLY TYR PHE GLY THR ILE LEU TYR SEQRES 10 L 342 THR GLY ASP PHE ARG TYR THR PRO SER MET LEU LYS GLU SEQRES 11 L 342 PRO ALA LEU THR LEU GLY LYS GLN ILE HIS THR LEU TYR SEQRES 12 L 342 LEU ASP ASN THR ASN CYS ASN PRO ALA LEU VAL LEU PRO SEQRES 13 L 342 SER ARG GLN GLU ALA ALA HIS GLN ILE VAL GLN LEU ILE SEQRES 14 L 342 ARG LYS HIS PRO GLN HIS ASN ILE LYS ILE GLY LEU TYR SEQRES 15 L 342 SER LEU GLY LYS GLU SER LEU LEU GLU GLN LEU ALA LEU SEQRES 16 L 342 GLU PHE GLN THR TRP VAL VAL LEU SER PRO ARG ARG LEU SEQRES 17 L 342 GLU LEU VAL GLN LEU LEU GLY LEU ALA ASP VAL PHE THR SEQRES 18 L 342 VAL GLU GLU LYS ALA GLY ARG ILE HIS ALA VAL ASP HIS SEQRES 19 L 342 MET GLU ILE CYS HIS SER ASN MET LEU ARG TRP ASN GLN SEQRES 20 L 342 THR HIS PRO THR ILE ALA ILE LEU PRO THR SER ARG LYS SEQRES 21 L 342 ILE HIS SER SER HIS PRO ASP ILE HIS VAL ILE PRO TYR SEQRES 22 L 342 SER ASP HIS SER SER TYR SER GLU LEU ARG ALA PHE VAL SEQRES 23 L 342 ALA ALA LEU LYS PRO CYS GLN VAL VAL PRO ILE VAL SER SEQRES 24 L 342 ARG ARG PRO CYS GLY GLY PHE GLN ASP SER LEU SER PRO SEQRES 25 L 342 ARG ILE SER VAL PRO LEU ILE PRO ASP SER VAL GLN GLN SEQRES 26 L 342 TYR MET SER SER SER SER ARG LYS PRO SER ALA GLU ASN SEQRES 27 L 342 LEU TYR PHE GLN MODRES 7A1F AME A 1 MET MODIFIED RESIDUE MODRES 7A1F AME L 1 MET MODIFIED RESIDUE HET AME A 1 23 HET AME L 1 23 HET FE A 401 1 HET NI A 402 1 HET D5M A 403 34 HET D5M A 404 34 HET FE L 401 1 HET NI L 402 1 HET D5M L 403 34 HET D5M L 404 34 HETNAM AME N-ACETYLMETHIONINE HETNAM FE FE (III) ION HETNAM NI NICKEL (II) ION HETNAM D5M 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE FORMUL 1 AME 2(C7 H13 N O3 S) FORMUL 3 FE 2(FE 3+) FORMUL 4 NI 2(NI 2+) FORMUL 5 D5M 4(C10 H14 N5 O6 P) FORMUL 11 HOH *566(H2 O) HELIX 1 AA1 SER A 17 ALA A 21 5 5 HELIX 2 AA2 HIS A 33 THR A 37 5 5 HELIX 3 AA3 SER A 51 GLN A 63 1 13 HELIX 4 AA4 SER A 65 GLN A 67 5 3 HELIX 5 AA5 THR A 124 LYS A 129 1 6 HELIX 6 AA6 GLU A 130 THR A 134 5 5 HELIX 7 AA7 SER A 157 LYS A 171 1 15 HELIX 8 AA8 LYS A 186 PHE A 197 1 12 HELIX 9 AA9 SER A 204 GLN A 212 1 9 HELIX 10 AB1 MET A 235 ILE A 237 5 3 HELIX 11 AB2 CYS A 238 ASN A 246 1 9 HELIX 12 AB3 SER A 278 LYS A 290 1 13 HELIX 13 AB4 PHE A 306 LEU A 310 5 5 HELIX 14 AB5 PRO A 320 SER A 328 1 9 HELIX 15 AB6 SER L 17 ALA L 21 5 5 HELIX 16 AB7 HIS L 33 THR L 37 5 5 HELIX 17 AB8 SER L 51 GLN L 63 1 13 HELIX 18 AB9 SER L 65 GLN L 67 5 3 HELIX 19 AC1 THR L 124 LYS L 129 1 6 HELIX 20 AC2 GLU L 130 THR L 134 5 5 HELIX 21 AC3 SER L 157 LYS L 171 1 15 HELIX 22 AC4 LYS L 186 PHE L 197 1 12 HELIX 23 AC5 SER L 204 GLN L 212 1 9 HELIX 24 AC6 MET L 235 ILE L 237 5 3 HELIX 25 AC7 CYS L 238 ASN L 246 1 9 HELIX 26 AC8 SER L 278 LYS L 290 1 13 HELIX 27 AC9 PHE L 306 LEU L 310 5 5 HELIX 28 AD1 PRO L 320 SER L 328 1 9 HELIX 29 AD2 SER L 329 LYS L 333 5 5 SHEET 1 AA1 5 VAL A 4 LEU A 5 0 SHEET 2 AA1 5 ILE A 11 VAL A 13 -1 O VAL A 13 N VAL A 4 SHEET 3 AA1 5 LEU A 26 PHE A 28 1 O LEU A 26 N ALA A 12 SHEET 4 AA1 5 LEU A 48 CYS A 50 1 O TYR A 49 N PHE A 27 SHEET 5 AA1 5 ILE A 69 ALA A 71 1 O GLN A 70 N LEU A 48 SHEET 1 AA2 6 SER A 77 PRO A 81 0 SHEET 2 AA2 6 THR A 89 ASP A 96 -1 O MET A 90 N LEU A 80 SHEET 3 AA2 6 VAL A 104 GLY A 110 -1 O MET A 105 N LEU A 95 SHEET 4 AA2 6 GLY A 113 TYR A 117 -1 O ILE A 115 N PHE A 108 SHEET 5 AA2 6 THR A 141 LEU A 144 1 O TYR A 143 N LEU A 116 SHEET 6 AA2 6 GLN A 293 PRO A 296 1 O GLN A 293 N LEU A 142 SHEET 1 AA3 6 PHE A 220 THR A 221 0 SHEET 2 AA3 6 VAL A 201 VAL A 202 1 N VAL A 201 O THR A 221 SHEET 3 AA3 6 ILE A 229 ASP A 233 1 O ILE A 229 N VAL A 202 SHEET 4 AA3 6 ASN A 176 LEU A 181 1 N ILE A 179 O HIS A 230 SHEET 5 AA3 6 THR A 251 PRO A 256 1 O ILE A 254 N LYS A 178 SHEET 6 AA3 6 ILE A 268 ILE A 271 1 O HIS A 269 N LEU A 255 SHEET 1 AA4 5 VAL L 4 LEU L 5 0 SHEET 2 AA4 5 ILE L 11 VAL L 13 -1 O VAL L 13 N VAL L 4 SHEET 3 AA4 5 LEU L 26 PHE L 28 1 O LEU L 26 N ALA L 12 SHEET 4 AA4 5 LEU L 48 CYS L 50 1 O TYR L 49 N PHE L 27 SHEET 5 AA4 5 ILE L 69 ALA L 71 1 O GLN L 70 N LEU L 48 SHEET 1 AA5 6 SER L 77 PRO L 81 0 SHEET 2 AA5 6 THR L 89 ASP L 96 -1 O MET L 90 N LEU L 80 SHEET 3 AA5 6 VAL L 104 GLY L 110 -1 O MET L 105 N LEU L 95 SHEET 4 AA5 6 GLY L 113 TYR L 117 -1 O ILE L 115 N PHE L 108 SHEET 5 AA5 6 THR L 141 LEU L 144 1 O TYR L 143 N LEU L 116 SHEET 6 AA5 6 GLN L 293 PRO L 296 1 O GLN L 293 N LEU L 142 SHEET 1 AA6 6 PHE L 220 THR L 221 0 SHEET 2 AA6 6 VAL L 201 VAL L 202 1 N VAL L 201 O THR L 221 SHEET 3 AA6 6 ILE L 229 ASP L 233 1 O ILE L 229 N VAL L 202 SHEET 4 AA6 6 ASN L 176 LEU L 181 1 N ILE L 177 O HIS L 230 SHEET 5 AA6 6 THR L 251 PRO L 256 1 O ILE L 254 N LYS L 178 SHEET 6 AA6 6 ILE L 268 ILE L 271 1 O HIS L 269 N ALA L 253 LINK C AME A 1 N ASN A 2 1555 1555 1.32 LINK C AME L 1 N ASN L 2 1555 1555 1.33 LINK NE2 HIS A 31 NI NI A 402 1555 1555 2.22 LINK ND1 HIS A 33 NI NI A 402 1555 1555 2.19 LINK OD2 ASP A 35 FE FE A 401 1555 1555 2.24 LINK NE2 HIS A 36 FE FE A 401 1555 1555 2.16 LINK NE2 HIS A 99 NI NI A 402 1555 1555 2.23 LINK OD2 ASP A 120 FE FE A 401 1555 1555 2.27 LINK OD2 ASP A 120 NI NI A 402 1555 1555 2.30 LINK FE FE A 401 O3P D5M A 404 1555 1555 2.26 LINK FE FE A 401 O HOH A 547 1555 1555 2.08 LINK FE FE A 401 O HOH A 548 1555 1555 2.24 LINK NI NI A 402 O2P D5M A 404 1555 1555 2.10 LINK NI NI A 402 O HOH A 547 1555 1555 1.86 LINK NE2 HIS L 31 NI NI L 402 1555 1555 2.31 LINK ND1 HIS L 33 NI NI L 402 1555 1555 2.04 LINK OD2 ASP L 35 FE FE L 401 1555 1555 2.25 LINK NE2 HIS L 36 FE FE L 401 1555 1555 2.18 LINK NE2 HIS L 99 NI NI L 402 1555 1555 2.22 LINK OD2 ASP L 120 FE FE L 401 1555 1555 2.22 LINK OD2 ASP L 120 NI NI L 402 1555 1555 2.26 LINK FE FE L 401 O1P D5M L 404 1555 1555 2.27 LINK FE FE L 401 O HOH L 557 1555 1555 1.88 LINK FE FE L 401 O HOH L 559 1555 1555 2.16 LINK NI NI L 402 O3P D5M L 404 1555 1555 2.16 LINK NI NI L 402 O HOH L 557 1555 1555 2.11 CRYST1 50.121 54.183 72.109 75.48 74.33 63.09 P 1 2 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 0.019952 -0.010127 -0.004125 0.00000 SCALE2 0.000000 0.020697 -0.003135 0.00000 SCALE3 0.000000 0.000000 0.014567 0.00000 HETATM 1 CT2 AME A 1 0.372 -9.586 -9.578 1.00 45.90 C HETATM 2 CT1 AME A 1 1.876 -9.621 -9.795 1.00 48.62 C HETATM 3 OT AME A 1 2.353 -8.954 -10.649 1.00 67.32 O HETATM 4 CB AME A 1 2.049 -12.760 -8.322 1.00 52.76 C HETATM 5 CG AME A 1 1.211 -13.570 -7.324 1.00 54.53 C HETATM 6 SD AME A 1 2.171 -14.081 -5.850 1.00 67.04 S HETATM 7 CE AME A 1 3.950 -14.263 -6.189 1.00 51.35 C HETATM 8 C AME A 1 3.329 -11.158 -6.840 1.00 50.59 C HETATM 9 O AME A 1 4.552 -11.221 -7.154 1.00 47.26 O HETATM 10 N AME A 1 2.739 -10.462 -8.991 1.00 54.48 N HETATM 11 CA AME A 1 2.248 -11.298 -7.905 1.00 52.75 C HETATM 12 HT23 AME A 1 -0.047 -9.083 -10.294 1.00 55.08 H HETATM 13 HT22 AME A 1 0.025 -10.492 -9.573 1.00 55.08 H HETATM 14 HT21 AME A 1 0.178 -9.161 -8.728 1.00 55.08 H HETATM 15 HB2 AME A 1 2.920 -13.179 -8.408 1.00 63.31 H HETATM 16 HB1 AME A 1 1.608 -12.779 -9.185 1.00 63.31 H HETATM 17 HG2 AME A 1 0.883 -14.365 -7.772 1.00 65.43 H HETATM 18 HG1 AME A 1 0.455 -13.033 -7.038 1.00 65.43 H HETATM 19 HE3 AME A 1 4.407 -14.536 -5.378 1.00 61.62 H HETATM 20 HE2 AME A 1 4.081 -14.934 -6.876 1.00 61.62 H HETATM 21 HE1 AME A 1 4.309 -13.415 -6.493 1.00 61.62 H HETATM 22 HN1 AME A 1 3.585 -10.445 -9.144 1.00 65.38 H HETATM 23 HA AME A 1 1.412 -10.939 -7.570 1.00 63.30 H