HEADER HYDROLASE 25-FEB-13 4JDG TITLE STRUCTURE OF TOMATO BIFUNCTIONAL NUCLEASE TBN1, VARIANT N211D COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PUTATIVE ENDONUCLEASE; COMPND 5 EC: 3.1.30.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SOLANUM LYCOPERSICUM; SOURCE 3 ORGANISM_COMMON: TOMATO; SOURCE 4 ORGANISM_TAXID: 4081; SOURCE 5 GENE: TBN1; SOURCE 6 EXPRESSION_SYSTEM: NICOTIANA BENTHAMIANA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLV07 KEYWDS MAINLY ALPHA HELICAL, TRINUCLEAR METAL CENTRE, MULTI-FUNCTIONAL, KEYWDS 2 NUCLEASE, 3'-NUCLEOTIDASE, HYDROLASE, GLYCOSYLATED, CYTOSOL MEMBRANE KEYWDS 3 ASSOCIATED EXPDTA X-RAY DIFFRACTION AUTHOR J.STRANSKY,J.DOHNALEK,T.KOVAL,T.PODZIMEK,P.LIPOVOVA,J.MATOUSEK REVDAT 4 08-NOV-23 4JDG 1 HETSYN REVDAT 3 29-JUL-20 4JDG 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 18-NOV-15 4JDG 1 JRNL REVDAT 1 26-FEB-14 4JDG 0 JRNL AUTH J.STRANSKY,T.KOVAL,T.PODZIMEK,A.TYCOVA,P.LIPOVOVA, JRNL AUTH 2 J.MATOUSEK,P.KOLENKO,K.FEJFAROVA,J.DUSKOVA,T.SKALOVA, JRNL AUTH 3 J.HASEK,J.DOHNALEK JRNL TITL PHOSPHATE BINDING IN THE ACTIVE CENTRE OF TOMATO JRNL TITL 2 MULTIFUNCTIONAL NUCLEASE TBN1 AND ANALYSIS OF SUPERHELIX JRNL TITL 3 FORMATION BY THE ENZYME JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 71 1408 2015 JRNL REFN ESSN 1744-3091 JRNL PMID 26527269 JRNL DOI 10.1107/S2053230X15018324 REMARK 2 REMARK 2 RESOLUTION. 2.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : CCP4 STEREOCHEMISTRY LIBRARY, VERSION 6.3.0 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 9432 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : RFREE THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 475 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.74 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 552 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 31 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2145 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 97 REMARK 3 SOLVENT ATOMS : 26 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.38000 REMARK 3 B12 (A**2) : 0.12000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.435 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.152 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.371 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 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): 2317 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2076 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3154 ; 1.413 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4748 ; 0.807 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 267 ; 5.579 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;36.427 ;23.966 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 362 ;15.035 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;16.188 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 344 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2576 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 563 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1068 ; 3.396 ; 5.848 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1067 ; 3.393 ; 5.845 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1335 ; 5.309 ; 8.762 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1336 ; 5.307 ; 8.765 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1249 ; 3.432 ; 6.100 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1245 ; 3.408 ; 6.105 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1814 ; 5.325 ; 9.090 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2837 ; 7.602 ;47.826 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2834 ; 7.603 ;47.820 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 REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4JDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077907. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.91841 REMARK 200 MONOCHROMATOR : KMC-1, SI (111) REMARK 200 OPTICS : 2 MIRRORS AND A DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9433 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.740 REMARK 200 RESOLUTION RANGE LOW (A) : 59.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.53600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.540 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: 4DJ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, 10% PEG 8000, 0.01M 5' REMARK 280 -AMP, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 57.97200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.47015 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.90433 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.97200 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.47015 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 24.90433 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.97200 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.47015 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.90433 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.94030 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 49.80867 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.94030 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 49.80867 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.94030 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 49.80867 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 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 ALA A 292 REMARK 465 SER A 293 REMARK 465 GLN A 294 REMARK 465 GLN A 295 REMARK 465 GLU A 296 REMARK 465 ASP A 297 REMARK 465 SER A 298 REMARK 465 VAL A 299 REMARK 465 VAL A 300 REMARK 465 ALA A 301 REMARK 465 THR A 302 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 43 -176.88 -67.78 REMARK 500 TYR A 57 -4.94 -58.00 REMARK 500 LYS A 92 -7.00 61.91 REMARK 500 ASP A 110 -11.82 80.67 REMARK 500 ASP A 133 -123.09 51.41 REMARK 500 PHE A 174 -111.96 61.88 REMARK 500 SER A 178 -162.83 -177.30 REMARK 500 ARG A 186 -43.53 -152.74 REMARK 500 LYS A 199 -2.80 67.99 REMARK 500 SER A 260 -164.71 -117.50 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 26 O REMARK 620 2 TRP A 26 N 77.1 REMARK 620 3 HIS A 31 NE2 86.9 112.6 REMARK 620 4 ASP A 151 OD1 165.2 88.3 100.9 REMARK 620 5 PO4 A 601 O1 84.4 65.2 171.3 87.5 REMARK 620 6 PO4 A 601 O3 73.8 125.3 111.0 114.1 66.6 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 HIS A 85 ND1 REMARK 620 2 HIS A 147 NE2 110.3 REMARK 620 3 ASP A 151 OD2 93.0 99.6 REMARK 620 4 PO4 A 601 O4 89.6 158.9 85.5 REMARK 620 5 PO4 A 601 O3 136.1 99.8 113.1 59.8 REMARK 620 N 1 2 3 4 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 ASP A 133 OD1 REMARK 620 2 HIS A 157 NE2 97.7 REMARK 620 3 HIS A 181 NE2 92.3 91.0 REMARK 620 4 ASP A 185 OD2 146.1 106.1 63.9 REMARK 620 5 ASP A 185 OD1 144.2 101.3 117.3 53.5 REMARK 620 6 PO4 A 601 O1 96.1 67.9 158.2 115.0 64.2 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SNG RELATED DB: PDB REMARK 900 WILD TYPE TBN1 REMARK 900 RELATED ID: 4DJ4 RELATED DB: PDB REMARK 900 ANOTHER CRYSTAL FORM OF MUTANT N211D DBREF 4JDG A 26 302 UNP Q0KFV0 Q0KFV0_SOLLC 26 302 SEQADV 4JDG ASP A 211 UNP Q0KFV0 ASN 211 ENGINEERED MUTATION SEQRES 1 A 277 TRP SER LYS GLU GLY HIS VAL MET THR CYS ARG ILE ALA SEQRES 2 A 277 GLN GLY LEU LEU ASN ASP GLU ALA ALA HIS ALA VAL LYS SEQRES 3 A 277 MET LEU LEU PRO GLU TYR VAL ASN GLY ASP LEU SER ALA SEQRES 4 A 277 LEU CYS VAL TRP PRO ASP GLN VAL ARG HIS TRP TYR LYS SEQRES 5 A 277 TYR LYS TRP THR SER PRO LEU HIS PHE ILE ASP THR PRO SEQRES 6 A 277 ASP LYS ALA CYS ASN PHE ASP TYR GLU ARG ASP CYS HIS SEQRES 7 A 277 ASP GLN HIS GLY VAL LYS ASP MET CYS VAL ALA GLY ALA SEQRES 8 A 277 ILE GLN ASN PHE THR THR GLN LEU SER HIS TYR ARG GLU SEQRES 9 A 277 GLY THR SER ASP ARG ARG TYR ASN MET THR GLU ALA LEU SEQRES 10 A 277 LEU PHE LEU SER HIS PHE MET GLY ASP ILE HIS GLN PRO SEQRES 11 A 277 MET HIS VAL GLY PHE THR SER ASP ALA GLY GLY ASN SER SEQRES 12 A 277 ILE ASP LEU ARG TRP PHE ARG HIS LYS SER ASN LEU HIS SEQRES 13 A 277 HIS VAL TRP ASP ARG GLU ILE ILE LEU THR ALA ALA LYS SEQRES 14 A 277 ASP TYR TYR ALA LYS ASP ILE ASN LEU LEU GLU GLU ASP SEQRES 15 A 277 ILE GLU GLY ASP PHE THR ASP GLY ILE TRP SER ASP ASP SEQRES 16 A 277 LEU ALA SER TRP ARG GLU CYS GLY ASN VAL PHE SER CYS SEQRES 17 A 277 VAL ASN LYS PHE ALA THR GLU SER ILE ASN ILE ALA CYS SEQRES 18 A 277 LYS TRP GLY TYR LYS GLY VAL GLU ALA GLY GLU THR LEU SEQRES 19 A 277 SER ASP ASP TYR PHE ASN SER ARG LEU PRO ILE VAL MET SEQRES 20 A 277 LYS ARG VAL ALA GLN GLY GLY ILE ARG LEU ALA MET LEU SEQRES 21 A 277 LEU ASN ASN VAL PHE GLY ALA SER GLN GLN GLU ASP SER SEQRES 22 A 277 VAL VAL ALA THR MODRES 4JDG ASN A 119 ASN GLYCOSYLATION SITE MODRES 4JDG ASN A 137 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET ZN A 401 1 HET ZN A 402 1 HET ZN A 403 1 HET PO4 A 601 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM ZN ZINC ION HETNAM PO4 PHOSPHATE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 2 BMA 2(C6 H12 O6) FORMUL 3 MAN C6 H12 O6 FORMUL 4 ZN 3(ZN 2+) FORMUL 7 PO4 O4 P 3- FORMUL 8 HOH *26(H2 O) HELIX 1 1 SER A 27 LEU A 41 1 15 HELIX 2 2 ASN A 43 LEU A 54 1 12 HELIX 3 3 PRO A 55 ASN A 59 5 5 HELIX 4 4 ASP A 61 LEU A 65 5 5 HELIX 5 5 VAL A 67 VAL A 72 1 6 HELIX 6 6 ARG A 73 TRP A 75 5 3 HELIX 7 7 TYR A 78 PHE A 86 5 9 HELIX 8 8 ASP A 97 CYS A 102 1 6 HELIX 9 9 CYS A 112 SER A 125 1 14 HELIX 10 10 ASN A 137 GLN A 154 1 18 HELIX 11 11 PRO A 155 GLY A 159 5 5 HELIX 12 12 ASP A 163 ASN A 167 5 5 HELIX 13 13 LEU A 180 ARG A 186 1 7 HELIX 14 14 ARG A 186 ALA A 198 1 13 HELIX 15 15 ASP A 200 ASP A 214 1 15 HELIX 16 16 TRP A 217 ASP A 219 5 3 HELIX 17 17 ASP A 220 ARG A 225 1 6 HELIX 18 18 ASN A 229 TRP A 248 1 20 HELIX 19 19 SER A 260 GLY A 291 1 32 SHEET 1 A 3 HIS A 176 ASN A 179 0 SHEET 2 A 3 ASP A 170 TRP A 173 -1 N TRP A 173 O HIS A 176 SHEET 3 A 3 THR A 258 LEU A 259 1 O LEU A 259 N ARG A 172 SSBOND 1 CYS A 35 CYS A 66 1555 1555 2.03 SSBOND 2 CYS A 94 CYS A 246 1555 1555 2.03 SSBOND 3 CYS A 102 CYS A 112 1555 1555 2.07 SSBOND 4 CYS A 227 CYS A 233 1555 1555 2.05 LINK ND2 ASN A 119 C1 NAG B 1 1555 1555 1.43 LINK ND2 ASN A 137 C1 NAG C 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.43 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.45 LINK O6 BMA C 3 C1 MAN C 4 1555 1555 1.45 LINK O TRP A 26 ZN ZN A 401 1555 1555 2.08 LINK N TRP A 26 ZN ZN A 401 1555 1555 2.29 LINK NE2 HIS A 31 ZN ZN A 401 1555 1555 1.88 LINK ND1 HIS A 85 ZN ZN A 402 1555 1555 2.20 LINK OD1 ASP A 133 ZN ZN A 403 5555 1555 2.30 LINK NE2 HIS A 147 ZN ZN A 402 1555 1555 2.15 LINK OD1 ASP A 151 ZN ZN A 401 1555 1555 2.10 LINK OD2 ASP A 151 ZN ZN A 402 1555 1555 2.19 LINK NE2 HIS A 157 ZN ZN A 403 1555 1555 2.37 LINK NE2 HIS A 181 ZN ZN A 403 1555 1555 2.35 LINK OD2 ASP A 185 ZN ZN A 403 1555 1555 2.34 LINK OD1 ASP A 185 ZN ZN A 403 1555 1555 2.51 LINK ZN ZN A 401 O1 PO4 A 601 1555 1555 2.25 LINK ZN ZN A 401 O3 PO4 A 601 1555 1555 2.25 LINK ZN ZN A 402 O4 PO4 A 601 1555 1555 2.21 LINK ZN ZN A 402 O3 PO4 A 601 1555 1555 2.62 LINK ZN ZN A 403 O1 PO4 A 601 1555 1555 2.57 CRYST1 115.944 115.944 74.713 90.00 90.00 120.00 H 3 9 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 0.008625 0.004980 0.000000 0.00000 SCALE2 0.000000 0.009959 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013385 0.00000