PDB Short entry for 3VUY HEADER PROTEIN BINDING/METAL BINDING PROTEIN 09-JUL-12 3VUY TITLE CRYSTAL STRUCTURE OF A20 ZF7 IN COMPLEX WITH LINEAR TETRAUBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYUBIQUITIN-C; COMPND 3 CHAIN: A, C, B; COMPND 4 FRAGMENT: UBIQUITIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3; COMPND 8 CHAIN: D, F, E; COMPND 9 FRAGMENT: A20-TYPE 7 ZINC FINGER DOMAIN, RESIDUES 757-790; COMPND 10 SYNONYM: TNF ALPHA-INDUCED PROTEIN 3, OTU DOMAIN-CONTAINING PROTEIN COMPND 11 7C, PUTATIVE DNA-BINDING PROTEIN A20, ZINC FINGER PROTEIN A20; COMPND 12 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: UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: TNFAIP3; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS ZINC FINGER, PROTEIN BINDING-METAL BINDING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.NISHIMASU,R.ISHITANI,O.NUREKI REVDAT 2 20-MAR-24 3VUY 1 REMARK SEQADV LINK REVDAT 1 13-FEB-13 3VUY 0 JRNL AUTH F.TOKUNAGA,H.NISHIMASU,R.ISHITANI,E.GOTO,T.NOGUCHI,K.MIO, JRNL AUTH 2 K.KAMEI,A.MA,K.IWAI,O.NUREKI JRNL TITL SPECIFIC RECOGNITION OF LINEAR POLYUBIQUITIN BY A20 ZINC JRNL TITL 2 FINGER 7 IS INVOLVED IN NF-KAPPAB REGULATION JRNL REF EMBO J. V. 31 3856 2012 JRNL REFN ISSN 0261-4189 JRNL PMID 23032187 JRNL DOI 10.1038/EMBOJ.2012.241 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 25820 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1288 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 45.6904 - 4.1196 1.00 2719 141 0.1717 0.2098 REMARK 3 2 4.1196 - 3.2701 1.00 2736 143 0.1686 0.1973 REMARK 3 3 3.2701 - 2.8568 1.00 2714 148 0.1958 0.2486 REMARK 3 4 2.8568 - 2.5956 1.00 2732 145 0.2233 0.2662 REMARK 3 5 2.5956 - 2.4096 1.00 2740 142 0.2411 0.2987 REMARK 3 6 2.4096 - 2.2675 1.00 2727 143 0.2539 0.2737 REMARK 3 7 2.2675 - 2.1540 1.00 2729 144 0.2791 0.3156 REMARK 3 8 2.1540 - 2.0602 1.00 2724 139 0.3248 0.3837 REMARK 3 9 2.0602 - 1.9809 0.99 2711 143 0.3738 0.3938 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 38.68 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.680 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.08410 REMARK 3 B22 (A**2) : 5.08410 REMARK 3 B33 (A**2) : -10.16820 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.012 2591 REMARK 3 ANGLE : 0.627 3461 REMARK 3 CHIRALITY : 0.046 380 REMARK 3 PLANARITY : 0.002 455 REMARK 3 DIHEDRAL : 14.097 989 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:76) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9448 28.5367 -12.6407 REMARK 3 T TENSOR REMARK 3 T11: 0.2336 T22: 0.4781 REMARK 3 T33: 0.1983 T12: -0.1107 REMARK 3 T13: 0.0039 T23: 0.0338 REMARK 3 L TENSOR REMARK 3 L11: 2.2150 L22: 4.2618 REMARK 3 L33: 2.3690 L12: 0.5223 REMARK 3 L13: -0.9139 L23: 0.5876 REMARK 3 S TENSOR REMARK 3 S11: 0.0937 S12: -0.0544 S13: -0.0860 REMARK 3 S21: 0.2157 S22: 0.0538 S23: 0.3427 REMARK 3 S31: 0.3819 S32: -0.7265 S33: -0.1472 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESID 1:76) REMARK 3 ORIGIN FOR THE GROUP (A): 6.8511 -2.3236 7.7800 REMARK 3 T TENSOR REMARK 3 T11: 0.3923 T22: 0.3176 REMARK 3 T33: 0.2670 T12: -0.0266 REMARK 3 T13: 0.0492 T23: 0.0794 REMARK 3 L TENSOR REMARK 3 L11: 7.6598 L22: 3.2130 REMARK 3 L33: 6.8955 L12: 1.1150 REMARK 3 L13: 0.3078 L23: 0.5356 REMARK 3 S TENSOR REMARK 3 S11: -0.1618 S12: -0.0313 S13: -0.4536 REMARK 3 S21: -0.2710 S22: 0.0943 S23: -0.4324 REMARK 3 S31: 0.6840 S32: 0.5412 S33: 0.0932 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN C AND RESID 1:76) REMARK 3 ORIGIN FOR THE GROUP (A): 28.4212 10.3667 8.9544 REMARK 3 T TENSOR REMARK 3 T11: 0.1163 T22: 0.3689 REMARK 3 T33: 0.2170 T12: 0.0215 REMARK 3 T13: 0.0213 T23: 0.0647 REMARK 3 L TENSOR REMARK 3 L11: 3.4754 L22: 5.8069 REMARK 3 L33: 3.7777 L12: 2.6450 REMARK 3 L13: 0.9910 L23: 0.0344 REMARK 3 S TENSOR REMARK 3 S11: -0.1455 S12: -0.2236 S13: -0.2336 REMARK 3 S21: -0.3283 S22: 0.0707 S23: -0.2374 REMARK 3 S31: 0.1785 S32: 0.3167 S33: 0.0234 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN D AND (RESID 757:789 OR RESID 801:802) ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.6684 31.8925 -29.6266 REMARK 3 T TENSOR REMARK 3 T11: 0.2666 T22: 0.4207 REMARK 3 T33: 0.2325 T12: -0.1753 REMARK 3 T13: -0.0246 T23: 0.0459 REMARK 3 L TENSOR REMARK 3 L11: 2.1759 L22: 1.8761 REMARK 3 L33: 5.9257 L12: -0.1503 REMARK 3 L13: 0.2901 L23: -0.4009 REMARK 3 S TENSOR REMARK 3 S11: 0.1829 S12: -0.3374 S13: -0.1752 REMARK 3 S21: 0.0009 S22: -0.1809 S23: -0.1598 REMARK 3 S31: 0.0981 S32: 0.5282 S33: -0.0223 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN E AND (RESID 759:790 OR RESID 801:802) ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.3542 7.3509 -8.5294 REMARK 3 T TENSOR REMARK 3 T11: 0.5193 T22: 0.2518 REMARK 3 T33: 0.1990 T12: -0.0081 REMARK 3 T13: 0.0326 T23: -0.0180 REMARK 3 L TENSOR REMARK 3 L11: 8.2677 L22: 8.0050 REMARK 3 L33: 7.9979 L12: -2.2778 REMARK 3 L13: -0.5569 L23: 1.9535 REMARK 3 S TENSOR REMARK 3 S11: -0.1851 S12: -0.2351 S13: 0.2044 REMARK 3 S21: 0.1420 S22: 0.1445 S23: -0.0825 REMARK 3 S31: -0.1035 S32: 0.4075 S33: 0.0164 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN F AND (RESID 759:789 OR RESID 801:802) ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.7408 20.2742 25.1040 REMARK 3 T TENSOR REMARK 3 T11: 0.4656 T22: 0.4691 REMARK 3 T33: 0.2742 T12: 0.1930 REMARK 3 T13: -0.0887 T23: -0.0295 REMARK 3 L TENSOR REMARK 3 L11: 3.6120 L22: 4.0328 REMARK 3 L33: 4.5592 L12: -1.7014 REMARK 3 L13: -0.9083 L23: -0.7841 REMARK 3 S TENSOR REMARK 3 S11: 0.0506 S12: 0.1590 S13: 0.2859 REMARK 3 S21: -0.0559 S22: -0.0027 S23: 0.2244 REMARK 3 S31: -0.7554 S32: -0.7649 S33: -0.0666 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 3VUY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000095531. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25855 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.47900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM TRIS-HCL, 150MM NACL, 0.2M NA/K REMARK 280 TARTRATE, 8% PEG 3350, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,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 28.45167 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 56.90333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 1480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, F 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: 3 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: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, E 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 GLY D 756 REMARK 465 GLY D 790 REMARK 465 GLY F 756 REMARK 465 PRO F 757 REMARK 465 PRO F 758 REMARK 465 GLY F 790 REMARK 465 GLY E 756 REMARK 465 PRO E 757 REMARK 465 PRO E 758 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 LYS D 759 CG CD CE NZ REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 GLN B 49 CG CD OE1 NE2 REMARK 470 GLU B 51 CG CD OE1 OE2 REMARK 470 ARG B 54 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 74 CG CD NE CZ NH1 NH2 REMARK 470 LYS E 759 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 O HOH C 112 O HOH C 136 2.00 REMARK 500 O HOH C 143 O HOH C 147 2.02 REMARK 500 O PHE F 770 O HOH F 911 2.04 REMARK 500 OE1 GLU B 64 O HOH B 115 2.06 REMARK 500 OE1 GLN C 49 O HOH C 142 2.17 REMARK 500 NH2 ARG A 42 O HOH A 125 2.18 REMARK 500 OG1 THR A 66 O HOH A 111 2.19 REMARK 500 O HOH A 160 O HOH D 913 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 N MET B 1 C GLY B 76 2555 1.33 REMARK 500 N MET C 1 C GLY C 76 3664 1.33 REMARK 500 N MET A 1 C GLY A 76 2665 1.33 REMARK 500 N MET A 1 O GLY A 76 2665 1.76 REMARK 500 N MET B 1 O GLY B 76 2555 2.13 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 D 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 762 SG REMARK 620 2 CYS D 767 SG 119.9 REMARK 620 3 CYS D 779 SG 115.3 110.7 REMARK 620 4 CYS D 782 SG 116.0 99.7 90.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K D 802 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 762 O REMARK 620 2 ALA D 764 O 87.4 REMARK 620 3 CYS D 767 O 98.9 91.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 762 SG REMARK 620 2 CYS F 767 SG 116.6 REMARK 620 3 CYS F 779 SG 116.8 114.1 REMARK 620 4 CYS F 782 SG 114.5 100.9 89.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K F 802 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 762 O REMARK 620 2 ALA F 764 O 95.6 REMARK 620 3 CYS F 767 O 111.9 90.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 762 SG REMARK 620 2 CYS E 767 SG 115.2 REMARK 620 3 CYS E 779 SG 117.0 117.1 REMARK 620 4 CYS E 782 SG 110.7 100.3 91.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K E 802 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 762 O REMARK 620 2 ALA E 764 O 83.2 REMARK 620 3 CYS E 767 O 101.6 89.2 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 D 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K D 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K F 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN E 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K E 802 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VUW RELATED DB: PDB REMARK 900 RELATED ID: 3VUX RELATED DB: PDB DBREF 3VUY A 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 3VUY D 757 790 UNP P21580 TNAP3_HUMAN 757 790 DBREF 3VUY C 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 3VUY F 757 790 UNP P21580 TNAP3_HUMAN 757 790 DBREF 3VUY B 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 3VUY E 757 790 UNP P21580 TNAP3_HUMAN 757 790 SEQADV 3VUY GLY D 756 UNP P21580 EXPRESSION TAG SEQADV 3VUY GLY F 756 UNP P21580 EXPRESSION TAG SEQADV 3VUY GLY E 756 UNP P21580 EXPRESSION TAG SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 D 35 GLY PRO PRO LYS GLN ARG CYS ARG ALA PRO ALA CYS ASP SEQRES 2 D 35 HIS PHE GLY ASN ALA LYS CYS ASN GLY TYR CYS ASN GLU SEQRES 3 D 35 CYS PHE GLN PHE LYS GLN MET TYR GLY SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 F 35 GLY PRO PRO LYS GLN ARG CYS ARG ALA PRO ALA CYS ASP SEQRES 2 F 35 HIS PHE GLY ASN ALA LYS CYS ASN GLY TYR CYS ASN GLU SEQRES 3 F 35 CYS PHE GLN PHE LYS GLN MET TYR GLY SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 E 35 GLY PRO PRO LYS GLN ARG CYS ARG ALA PRO ALA CYS ASP SEQRES 2 E 35 HIS PHE GLY ASN ALA LYS CYS ASN GLY TYR CYS ASN GLU SEQRES 3 E 35 CYS PHE GLN PHE LYS GLN MET TYR GLY HET ZN D 801 1 HET K D 802 1 HET ZN F 801 1 HET K F 802 1 HET ZN E 801 1 HET K E 802 1 HETNAM ZN ZINC ION HETNAM K POTASSIUM ION FORMUL 7 ZN 3(ZN 2+) FORMUL 8 K 3(K 1+) FORMUL 13 HOH *184(H2 O) HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 ASN D 772 ASN D 776 5 5 HELIX 4 4 CYS D 779 TYR D 789 1 11 HELIX 5 5 THR C 22 GLY C 35 1 14 HELIX 6 6 PRO C 37 ASP C 39 5 3 HELIX 7 7 CYS F 779 TYR F 789 1 11 HELIX 8 8 THR B 22 GLY B 35 1 14 HELIX 9 9 PRO B 37 ASP B 39 5 3 HELIX 10 10 ASN E 772 ASN E 776 5 5 HELIX 11 11 CYS E 779 GLY E 790 1 12 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 LYS A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 THR A 66 LEU A 71 1 O LEU A 67 N PHE A 4 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 B 5 THR C 12 GLU C 16 0 SHEET 2 B 5 GLN C 2 LYS C 6 -1 N ILE C 3 O LEU C 15 SHEET 3 B 5 THR C 66 LEU C 71 1 O LEU C 67 N PHE C 4 SHEET 4 B 5 GLN C 41 PHE C 45 -1 N ARG C 42 O VAL C 70 SHEET 5 B 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 SHEET 1 C 5 THR B 12 GLU B 16 0 SHEET 2 C 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 C 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 C 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 C 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK SG CYS D 762 ZN ZN D 801 1555 1555 2.68 LINK O CYS D 762 K K D 802 1555 1555 2.65 LINK O ALA D 764 K K D 802 1555 1555 2.72 LINK SG CYS D 767 ZN ZN D 801 1555 1555 2.67 LINK O CYS D 767 K K D 802 1555 1555 2.96 LINK SG CYS D 779 ZN ZN D 801 1555 1555 2.79 LINK SG CYS D 782 ZN ZN D 801 1555 1555 2.75 LINK SG CYS F 762 ZN ZN F 801 1555 1555 2.71 LINK O CYS F 762 K K F 802 1555 1555 2.31 LINK O ALA F 764 K K F 802 1555 1555 2.66 LINK SG CYS F 767 ZN ZN F 801 1555 1555 2.70 LINK O CYS F 767 K K F 802 1555 1555 2.75 LINK SG CYS F 779 ZN ZN F 801 1555 1555 2.80 LINK SG CYS F 782 ZN ZN F 801 1555 1555 2.80 LINK SG CYS E 762 ZN ZN E 801 1555 1555 2.75 LINK O CYS E 762 K K E 802 1555 1555 2.50 LINK O ALA E 764 K K E 802 1555 1555 2.84 LINK SG CYS E 767 ZN ZN E 801 1555 1555 2.71 LINK O CYS E 767 K K E 802 1555 1555 2.89 LINK SG CYS E 779 ZN ZN E 801 1555 1555 2.84 LINK SG CYS E 782 ZN ZN E 801 1555 1555 2.78 SITE 1 AC1 4 CYS D 762 CYS D 767 CYS D 779 CYS D 782 SITE 1 AC2 3 CYS D 762 ALA D 764 CYS D 767 SITE 1 AC3 4 CYS F 762 CYS F 767 CYS F 779 CYS F 782 SITE 1 AC4 3 CYS F 762 ALA F 764 CYS F 767 SITE 1 AC5 4 CYS E 762 CYS E 767 CYS E 779 CYS E 782 SITE 1 AC6 3 CYS E 762 ALA E 764 CYS E 767 CRYST1 62.438 62.438 85.355 90.00 90.00 120.00 P 31 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 0.016016 0.009247 0.000000 0.00000 SCALE2 0.000000 0.018494 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011716 0.00000