HEADER HYDROLASE 13-SEP-23 8QJQ TITLE SMNUC1 NUCLEASE FROM STENOTROPHOMONAS MALTOPHILIA IN COMPLEX WITH TITLE 2 CYTIDINE - 5' - MONOPHOSPHATE AS AN INHIBITOR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: S1/P1 NUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STENOTROPHOMONAS MALTOPHILIA; SOURCE 3 ORGANISM_TAXID: 40324; SOURCE 4 STRAIN: SANG_2012; SOURCE 5 GENE: A1OC_03585; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET303/CT-HIS_SMNUC1 KEYWDS NUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.ADAMKOVA,T.KOVAL,P.KOLENKO,J.DOHNALEK REVDAT 1 25-SEP-24 8QJQ 0 JRNL AUTH K.ADAMKOVA,M.TRUNDOVA,T.KOVAL,B.HUSTAKOVA,J.DUSKOVA, JRNL AUTH 2 T.SKALOVA,P.KOLENKO,J.DOHNALEK JRNL TITL SUBSTRATE PREFERENCE, RNA BINDING AND ACTIVE SITE JRNL TITL 2 VERSATILITY OF THE STENOTROPHOMONAS MALTOPHILIA NUCLEASE JRNL TITL 3 SMNUC1, EXPLAINED BY A STRUCTURAL STUDY JRNL REF THE FEBS JOURNAL 2024 JRNL DOI 10.1111/FEBS.17265 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 45328 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2212 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3250 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE SET COUNT : 0 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3890 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 188 REMARK 3 SOLVENT ATOMS : 418 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03100 REMARK 3 B22 (A**2) : -1.08700 REMARK 3 B33 (A**2) : 0.40900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.76900 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.464 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4207 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3864 ; 0.004 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5727 ; 1.408 ; 1.642 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8854 ; 1.351 ; 1.593 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 518 ; 6.613 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 259 ;29.218 ;20.811 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 669 ;13.754 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 47 ;18.024 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 511 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5247 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1027 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 987 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 141 ; 0.232 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1973 ; 0.155 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 306 ; 0.187 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 10 ; 0.072 ; 0.200 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): 2015 ; 2.114 ; 2.790 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2014 ; 2.113 ; 2.787 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2522 ; 3.259 ; 4.172 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2523 ; 3.258 ; 4.175 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2192 ; 2.674 ; 3.244 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2109 ; 2.469 ; 3.177 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3195 ; 4.053 ; 4.720 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3070 ; 3.932 ; 4.617 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 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 : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS. LAST REFINEMENT CYCLE WAS PERFORMED AGAINST REMARK 3 ALL REFLECTIONS. REMARK 4 REMARK 4 8QJQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1292132506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45358 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 41.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 1.05900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 25 % W/V PEG REMARK 280 3350, 0.2 M LITHIUM SULFATE, CRYO-PROTECTION 25% V/V GLYCEROL, REMARK 280 PROTEIN CONCENTRATION 7.5 MG/ML., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 36.58300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 HIS A 275 REMARK 465 HIS A 276 REMARK 465 HIS A 277 REMARK 465 HIS A 278 REMARK 465 HIS A 279 REMARK 465 HIS A 280 REMARK 465 HIS B 277 REMARK 465 HIS B 278 REMARK 465 HIS B 279 REMARK 465 HIS B 280 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 O HOH A 729 O HOH A 742 2.18 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 CYS A 105 36.90 -162.21 REMARK 500 CYS A 105 63.94 -167.40 REMARK 500 ASN A 169 47.67 -104.21 REMARK 500 SER A 180 -31.19 -154.14 REMARK 500 ARG A 272 -38.35 -144.30 REMARK 500 ASP B 60 -19.27 79.40 REMARK 500 CYS B 105 49.06 -147.81 REMARK 500 SER B 180 -35.55 -150.64 REMARK 500 SER B 180 -42.30 -147.52 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 B 668 DISTANCE = 5.96 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 27 N REMARK 620 2 TRP A 27 O 77.8 REMARK 620 3 HIS A 32 NE2 111.1 91.6 REMARK 620 4 ASP A 145 OD1 88.0 165.4 90.6 REMARK 620 5 C5P A 404 O3P 104.1 84.6 142.9 102.1 REMARK 620 6 HOH A 503 O 141.3 100.9 107.5 92.1 38.3 REMARK 620 N 1 2 3 4 5 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 ASP A 71 OD1 REMARK 620 2 HIS A 88 ND1 88.1 REMARK 620 3 HIS A 141 NE2 84.5 103.1 REMARK 620 4 ASP A 145 OD2 171.9 100.0 92.6 REMARK 620 5 C5P A 404 O2P 85.4 97.5 156.7 94.5 REMARK 620 6 HOH A 503 O 78.8 148.7 103.8 94.6 53.5 REMARK 620 N 1 2 3 4 5 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 151 NE2 REMARK 620 2 HIS A 175 NE2 96.8 REMARK 620 3 ASP A 179 OD1 92.8 98.1 REMARK 620 4 ASP A 179 OD2 148.7 93.0 56.3 REMARK 620 5 C5P A 404 O1P 101.9 119.7 136.8 98.8 REMARK 620 6 HOH A 501 O 90.8 165.1 94.3 87.0 45.8 REMARK 620 7 HOH A 502 O 93.1 92.7 167.0 116.1 30.3 74.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP B 27 N REMARK 620 2 TRP B 27 O 78.9 REMARK 620 3 HIS B 32 NE2 111.8 94.2 REMARK 620 4 ASP B 145 OD1 86.9 165.8 91.1 REMARK 620 5 PO4 B 415 O3 146.8 89.3 99.8 102.7 REMARK 620 6 PO4 B 415 O4 85.7 85.9 162.1 93.0 62.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 71 OD1 REMARK 620 2 HIS B 88 ND1 87.3 REMARK 620 3 HIS B 141 NE2 79.0 99.9 REMARK 620 4 ASP B 145 OD2 171.0 101.2 96.4 REMARK 620 5 PO4 B 415 O3 74.1 155.9 91.7 98.4 REMARK 620 6 PO4 B 415 O2 90.6 98.5 158.4 91.1 67.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 151 NE2 REMARK 620 2 HIS B 175 NE2 88.8 REMARK 620 3 ASP B 179 OD1 88.0 95.1 REMARK 620 4 ASP B 179 OD2 141.1 97.9 53.4 REMARK 620 5 C5P B 404 O1P 116.3 95.7 153.5 101.1 REMARK 620 6 PO4 B 415 O4 85.3 171.8 90.4 90.2 81.9 REMARK 620 N 1 2 3 4 5 DBREF 8QJQ A 27 272 UNP J7SYS2 J7SYS2_STEMA 27 272 DBREF 8QJQ B 27 272 UNP J7SYS2 J7SYS2_STEMA 27 272 SEQADV 8QJQ LEU A 273 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ GLU A 274 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ HIS A 275 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ HIS A 276 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ HIS A 277 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ HIS A 278 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ HIS A 279 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ HIS A 280 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ LEU B 273 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ GLU B 274 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ HIS B 275 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ HIS B 276 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ HIS B 277 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ HIS B 278 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ HIS B 279 UNP J7SYS2 EXPRESSION TAG SEQADV 8QJQ HIS B 280 UNP J7SYS2 EXPRESSION TAG SEQRES 1 A 254 TRP GLY ALA GLN GLY HIS ARG LEU VAL ALA GLU VAL ALA SEQRES 2 A 254 ASP ALA ARG LEU ASN PRO THR ALA ARG ALA GLU VAL ASP SEQRES 3 A 254 ARG LEU LEU ALA THR GLU PRO ASP ALA THR LEU ALA SER SEQRES 4 A 254 ILE ALA PRO TRP ALA ASP GLN LEU ARG ALA LYS ASP PRO SEQRES 5 A 254 GLY LEU GLY ARG ARG SER ALA GLY TRP HIS TYR VAL ASN SEQRES 6 A 254 ILE ALA GLU ASP ASN CYS HIS TYR GLU ALA PRO LYS HIS SEQRES 7 A 254 CYS ARG ASN GLY ASN CYS ILE VAL GLU ALA LEU LYS ALA SEQRES 8 A 254 GLN SER THR ILE LEU GLY ASP ARG SER LEU THR ASP GLY SEQRES 9 A 254 GLU ARG LEU GLN ALA LEU LYS PHE VAL VAL HIS LEU VAL SEQRES 10 A 254 GLY ASP ILE HIS GLN PRO MET HIS ALA GLY TYR ALA HIS SEQRES 11 A 254 ASP LYS GLY GLY ASN ASP PHE GLN LEU GLN PHE GLY ASN SEQRES 12 A 254 ARG GLY THR ASN LEU HIS SER LEU TRP ASP SER GLY MET SEQRES 13 A 254 LEU ASN THR ARG LYS LEU ASP ASP ALA GLY TYR LEU PRO SEQRES 14 A 254 LEU LEU GLN SER GLN ARG ALA PRO LYS LEU ALA ARG GLN SEQRES 15 A 254 SER ASN PRO GLN ARG ASP PRO GLN THR TRP ALA GLU ALA SEQRES 16 A 254 SER CYS ARG ILE SER MET GLN ALA GLY VAL TYR PRO ALA SEQRES 17 A 254 THR ARG LYS ILE GLY ASP GLU TYR THR GLU ARG TYR ARG SEQRES 18 A 254 PRO LEU ALA GLU ALA GLN LEU ARG LEU ALA GLY GLU ASN SEQRES 19 A 254 LEU ALA GLN LEU LEU ASN ARG VAL LEU GLY ALA ARG LEU SEQRES 20 A 254 GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 254 TRP GLY ALA GLN GLY HIS ARG LEU VAL ALA GLU VAL ALA SEQRES 2 B 254 ASP ALA ARG LEU ASN PRO THR ALA ARG ALA GLU VAL ASP SEQRES 3 B 254 ARG LEU LEU ALA THR GLU PRO ASP ALA THR LEU ALA SER SEQRES 4 B 254 ILE ALA PRO TRP ALA ASP GLN LEU ARG ALA LYS ASP PRO SEQRES 5 B 254 GLY LEU GLY ARG ARG SER ALA GLY TRP HIS TYR VAL ASN SEQRES 6 B 254 ILE ALA GLU ASP ASN CYS HIS TYR GLU ALA PRO LYS HIS SEQRES 7 B 254 CYS ARG ASN GLY ASN CYS ILE VAL GLU ALA LEU LYS ALA SEQRES 8 B 254 GLN SER THR ILE LEU GLY ASP ARG SER LEU THR ASP GLY SEQRES 9 B 254 GLU ARG LEU GLN ALA LEU LYS PHE VAL VAL HIS LEU VAL SEQRES 10 B 254 GLY ASP ILE HIS GLN PRO MET HIS ALA GLY TYR ALA HIS SEQRES 11 B 254 ASP LYS GLY GLY ASN ASP PHE GLN LEU GLN PHE GLY ASN SEQRES 12 B 254 ARG GLY THR ASN LEU HIS SER LEU TRP ASP SER GLY MET SEQRES 13 B 254 LEU ASN THR ARG LYS LEU ASP ASP ALA GLY TYR LEU PRO SEQRES 14 B 254 LEU LEU GLN SER GLN ARG ALA PRO LYS LEU ALA ARG GLN SEQRES 15 B 254 SER ASN PRO GLN ARG ASP PRO GLN THR TRP ALA GLU ALA SEQRES 16 B 254 SER CYS ARG ILE SER MET GLN ALA GLY VAL TYR PRO ALA SEQRES 17 B 254 THR ARG LYS ILE GLY ASP GLU TYR THR GLU ARG TYR ARG SEQRES 18 B 254 PRO LEU ALA GLU ALA GLN LEU ARG LEU ALA GLY GLU ASN SEQRES 19 B 254 LEU ALA GLN LEU LEU ASN ARG VAL LEU GLY ALA ARG LEU SEQRES 20 B 254 GLU HIS HIS HIS HIS HIS HIS HET ZN A 401 1 HET ZN A 402 1 HET ZN A 403 1 HET C5P A 404 21 HET GOL A 405 6 HET PEG A 406 7 HET GOL A 407 6 HET SO4 A 408 5 HET SO4 A 409 5 HET SO4 A 410 5 HET SO4 A 411 5 HET SO4 A 412 5 HET SO4 A 413 5 HET SO4 A 414 5 HET SO4 A 415 5 HET SO4 A 416 5 HET SO4 A 417 5 HET SO4 A 418 5 HET ZN B 401 1 HET ZN B 402 1 HET ZN B 403 1 HET C5P B 404 21 HET 1PE B 405 16 HET SO4 B 406 5 HET SO4 B 407 5 HET SO4 B 408 5 HET SO4 B 409 5 HET SO4 B 410 5 HET SO4 B 411 5 HET SO4 B 412 5 HET SO4 B 413 5 HET SO4 B 414 5 HET PO4 B 415 5 HETNAM ZN ZINC ION HETNAM C5P CYTIDINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM SO4 SULFATE ION HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 1PE PEG400 FORMUL 3 ZN 6(ZN 2+) FORMUL 6 C5P 2(C9 H14 N3 O8 P) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 8 PEG C4 H10 O3 FORMUL 10 SO4 20(O4 S 2-) FORMUL 25 1PE C10 H22 O6 FORMUL 35 PO4 O4 P 3- FORMUL 36 HOH *418(H2 O) HELIX 1 AA1 GLY A 28 ALA A 41 1 14 HELIX 2 AA2 ASN A 44 THR A 57 1 14 HELIX 3 AA3 THR A 62 ALA A 67 1 6 HELIX 4 AA4 PRO A 68 ASP A 77 1 10 HELIX 5 AA5 GLY A 79 SER A 84 1 6 HELIX 6 AA6 ALA A 85 TYR A 89 5 5 HELIX 7 AA7 ILE A 92 ASN A 96 5 5 HELIX 8 AA8 GLU A 100 CYS A 105 1 6 HELIX 9 AA9 CYS A 110 GLY A 123 1 14 HELIX 10 AB1 THR A 128 HIS A 147 1 20 HELIX 11 AB2 GLN A 148 GLY A 153 5 6 HELIX 12 AB3 LEU A 174 SER A 180 1 7 HELIX 13 AB4 SER A 180 THR A 185 1 6 HELIX 14 AB5 ASP A 189 GLN A 200 1 12 HELIX 15 AB6 ARG A 213 MET A 227 1 15 HELIX 16 AB7 GLY A 239 GLY A 270 1 32 HELIX 17 AB8 GLY B 28 ALA B 41 1 14 HELIX 18 AB9 ASN B 44 THR B 57 1 14 HELIX 19 AC1 THR B 62 ALA B 67 1 6 HELIX 20 AC2 PRO B 68 ASP B 71 5 4 HELIX 21 AC3 GLN B 72 ASP B 77 1 6 HELIX 22 AC4 ASP B 77 ALA B 85 1 9 HELIX 23 AC5 GLY B 86 TYR B 89 5 4 HELIX 24 AC6 ILE B 92 ASN B 96 5 5 HELIX 25 AC7 GLU B 100 CYS B 105 1 6 HELIX 26 AC8 CYS B 110 GLY B 123 1 14 HELIX 27 AC9 THR B 128 HIS B 147 1 20 HELIX 28 AD1 GLN B 148 GLY B 153 5 6 HELIX 29 AD2 LEU B 174 SER B 180 1 7 HELIX 30 AD3 SER B 180 THR B 185 1 6 HELIX 31 AD4 ASP B 189 SER B 199 1 11 HELIX 32 AD5 ARG B 213 MET B 227 1 15 HELIX 33 AD6 GLY B 239 GLY B 270 1 32 SHEET 1 AA1 3 GLY A 171 ASN A 173 0 SHEET 2 AA1 3 GLN A 164 PHE A 167 -1 N LEU A 165 O THR A 172 SHEET 3 AA1 3 LYS A 237 ILE A 238 1 O ILE A 238 N GLN A 166 SHEET 1 AA2 2 GLN B 164 PHE B 167 0 SHEET 2 AA2 2 ARG B 170 ASN B 173 -1 O THR B 172 N LEU B 165 SSBOND 1 CYS A 97 CYS A 223 1555 1555 2.04 SSBOND 2 CYS A 105 CYS A 110 1555 1555 2.03 SSBOND 3 CYS B 97 CYS B 223 1555 1555 2.03 SSBOND 4 CYS B 105 CYS B 110 1555 1555 2.06 LINK N TRP A 27 ZN ZN A 401 1555 1555 2.09 LINK O TRP A 27 ZN ZN A 401 1555 1555 2.18 LINK NE2 HIS A 32 ZN ZN A 401 1555 1555 2.04 LINK OD1 ASP A 71 ZN ZN A 402 1555 1555 2.31 LINK ND1 HIS A 88 ZN ZN A 402 1555 1555 2.05 LINK NE2 HIS A 141 ZN ZN A 402 1555 1555 2.09 LINK OD1 ASP A 145 ZN ZN A 401 1555 1555 2.11 LINK OD2 ASP A 145 ZN ZN A 402 1555 1555 2.08 LINK NE2 HIS A 151 ZN ZN A 403 1555 1555 2.01 LINK NE2 HIS A 175 ZN ZN A 403 1555 1555 2.06 LINK OD1 ASP A 179 ZN ZN A 403 1555 1555 2.52 LINK OD2 ASP A 179 ZN ZN A 403 1555 1555 2.14 LINK ZN ZN A 401 O3P C5P A 404 1555 1555 1.89 LINK ZN ZN A 401 O HOH A 503 1555 1555 2.22 LINK ZN ZN A 402 O2P C5P A 404 1555 1555 2.06 LINK ZN ZN A 402 O HOH A 503 1555 1555 2.05 LINK ZN ZN A 403 O1P C5P A 404 1555 1555 1.86 LINK ZN ZN A 403 O HOH A 501 1555 1555 1.96 LINK ZN ZN A 403 O HOH A 502 1555 1555 2.33 LINK N TRP B 27 ZN ZN B 401 1555 1555 2.09 LINK O TRP B 27 ZN ZN B 401 1555 1555 2.15 LINK NE2 HIS B 32 ZN ZN B 401 1555 1555 2.03 LINK OD1 ASP B 71 ZN ZN B 402 1555 1555 2.53 LINK ND1 HIS B 88 ZN ZN B 402 1555 1555 2.12 LINK NE2 HIS B 141 ZN ZN B 402 1555 1555 2.07 LINK OD1 ASP B 145 ZN ZN B 401 1555 1555 2.06 LINK OD2 ASP B 145 ZN ZN B 402 1555 1555 1.97 LINK NE2 HIS B 151 ZN ZN B 403 1555 1555 2.08 LINK NE2 HIS B 175 ZN ZN B 403 1555 1555 2.12 LINK OD1 ASP B 179 ZN ZN B 403 1555 1555 2.61 LINK OD2 ASP B 179 ZN ZN B 403 1555 1555 2.08 LINK ZN ZN B 401 O3 PO4 B 415 1555 1555 2.00 LINK ZN ZN B 401 O4 PO4 B 415 1555 1555 2.63 LINK ZN ZN B 402 O3 PO4 B 415 1555 1555 2.33 LINK ZN ZN B 402 O2 PO4 B 415 1555 1555 2.28 LINK ZN ZN B 403 O1P C5P B 404 1555 1555 2.04 LINK ZN ZN B 403 O4 PO4 B 415 1555 1555 2.20 CRYST1 43.255 73.166 81.660 90.00 104.99 90.00 P 1 21 1 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 0.023119 0.000000 0.006191 0.00000 SCALE2 0.000000 0.013668 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012677 0.00000