HEADER ENDOCYTOSIS 16-JUN-20 6ZE9 TITLE NON-NATIVE FOLD OF THE PUTATIVE VPS39 ZINC FINGER DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: VAM6/VPS39-LIKE PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: TRAP1-LIKE PROTEIN,HVAM6P; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: N-TERMINAL RESIDUES MHHHHHHM REPRESENT THE COMPND 7 HEXAHISTIDINE PURIFICATION TAG AND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: VPS39, KIAA0770, TLP, VAM6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: POPTH KEYWDS MEMBRANE TRAFFICKING, HOPS, ENDOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR B.G.BUTT,S.C.GRAHAM REVDAT 2 12-AUG-20 6ZE9 1 JRNL LINK REVDAT 1 24-JUN-20 6ZE9 0 JRNL AUTH B.G.BUTT,E.J.SCOURFIELD,S.C.GRAHAM JRNL TITL NON-NATIVE FOLD OF THE PUTATIVE VPS39 ZINC FINGER DOMAIN. JRNL REF WELLCOME OPEN RES V. 5 154 2020 JRNL REFN ISSN 2398-502X JRNL PMID 32724865 JRNL DOI 10.12688/WELLCOMEOPENRES.16078.1 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 5139 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 286 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2535 REMARK 3 BIN FREE R VALUE : 0.3028 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 18 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 922 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 1 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 92.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 122.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -14.60400 REMARK 3 B22 (A**2) : -14.60400 REMARK 3 B33 (A**2) : 29.20810 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.410 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.614 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.335 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.550 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.328 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.905 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 953 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1284 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 315 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 157 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 953 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 115 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : 12 ; 1.000 ; HARMONIC REMARK 3 UTILITY ANGLES : 15 ; 1.000 ; HARMONIC REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 585 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.07 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.65 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.60 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|-4 - A|848 } REMARK 3 ORIGIN FOR THE GROUP (A): 29.1015 33.387 14.3792 REMARK 3 T TENSOR REMARK 3 T11: 0.2695 T22: -0.1886 REMARK 3 T33: -0.0603 T12: 0.2467 REMARK 3 T13: 0.0418 T23: -0.1582 REMARK 3 L TENSOR REMARK 3 L11: 16.6309 L22: 4.3013 REMARK 3 L33: 5.7526 L12: 0.5013 REMARK 3 L13: 0.7651 L23: -1.8664 REMARK 3 S TENSOR REMARK 3 S11: 0.0606 S12: 0.6243 S13: -0.6213 REMARK 3 S21: 0.6243 S22: 0.0907 S23: -0.0299 REMARK 3 S31: -0.6213 S32: -0.0299 S33: -0.1513 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { A|849 - A|859 } REMARK 3 ORIGIN FOR THE GROUP (A): 48.1146 26.3234 5.5119 REMARK 3 T TENSOR REMARK 3 T11: -0.2744 T22: 0.6079 REMARK 3 T33: -0.2374 T12: 0.3014 REMARK 3 T13: 0.2021 T23: 0.0632 REMARK 3 L TENSOR REMARK 3 L11: 16.6309 L22: 16.4273 REMARK 3 L33: 3.7601 L12: -0 REMARK 3 L13: 2.8146 L23: -5.8208 REMARK 3 S TENSOR REMARK 3 S11: 0.1474 S12: 0.5241 S13: -0.4723 REMARK 3 S21: 0.5241 S22: 0.026 S23: 0.6639 REMARK 3 S31: -0.4723 S32: 0.6639 S33: -0.1734 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { A|1001 - A|1001 } REMARK 3 ORIGIN FOR THE GROUP (A): 23.7353 31.4499 15.9971 REMARK 3 T TENSOR REMARK 3 T11: 0.2101 T22: 0.1387 REMARK 3 T33: -0.0336 T12: 0.2153 REMARK 3 T13: 0.0021 T23: -0.1322 REMARK 3 L TENSOR REMARK 3 L11: 15.2652 L22: 1.8668 REMARK 3 L33: 1.5673 L12: -5.2597 REMARK 3 L13: 0.0413 L23: -1.062 REMARK 3 S TENSOR REMARK 3 S11: 0.3715 S12: 0.4675 S13: 0.0563 REMARK 3 S21: 0.4675 S22: 0.2286 S23: -0.2159 REMARK 3 S31: 0.0563 S32: -0.2159 S33: -0.6001 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { B|-4 - B|848 } REMARK 3 ORIGIN FOR THE GROUP (A): 5.3527 52.8245 18.1416 REMARK 3 T TENSOR REMARK 3 T11: -0.2828 T22: 0.2604 REMARK 3 T33: 0.1106 T12: 0.0834 REMARK 3 T13: -0.0439 T23: 0.2588 REMARK 3 L TENSOR REMARK 3 L11: 3.5779 L22: 4.2642 REMARK 3 L33: 8.1919 L12: 0.5775 REMARK 3 L13: -3.7682 L23: 1.0552 REMARK 3 S TENSOR REMARK 3 S11: 0.0338 S12: -0.7737 S13: -0.1002 REMARK 3 S21: -0.7737 S22: -1.0546 S23: 0.4559 REMARK 3 S31: -0.1002 S32: 0.4559 S33: 1.0208 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: { B|849 - B|859 } REMARK 3 ORIGIN FOR THE GROUP (A): -13.2447 60.8195 27.6767 REMARK 3 T TENSOR REMARK 3 T11: -0.1985 T22: 0.2336 REMARK 3 T33: 0.0118 T12: 0.1688 REMARK 3 T13: 0.053 T23: -0.1795 REMARK 3 L TENSOR REMARK 3 L11: 7.3702 L22: 7.4218 REMARK 3 L33: 16.6309 L12: -4.7737 REMARK 3 L13: 2.706 L23: -0.1105 REMARK 3 S TENSOR REMARK 3 S11: -0.0177 S12: 0.434 S13: -0.9111 REMARK 3 S21: 0.434 S22: 0.0695 S23: 0.036 REMARK 3 S31: -0.9111 S32: 0.036 S33: -0.0518 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: { B|1001 - B|1001 } REMARK 3 ORIGIN FOR THE GROUP (A): 8.2139 51.9784 13.0254 REMARK 3 T TENSOR REMARK 3 T11: -0.2156 T22: 0.1745 REMARK 3 T33: 0.032 T12: 0.0691 REMARK 3 T13: 0.0298 T23: 0.2432 REMARK 3 L TENSOR REMARK 3 L11: 6.7509 L22: 1.7576 REMARK 3 L33: 8.8183 L12: -3.4058 REMARK 3 L13: -3.4489 L23: 2.1635 REMARK 3 S TENSOR REMARK 3 S11: 0.2269 S12: -0.3458 S13: 0.1326 REMARK 3 S21: -0.3458 S22: -0.8281 S23: 0.5681 REMARK 3 S31: 0.1326 S32: 0.5681 S33: 0.6012 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: { C|-3 - C|848 } REMARK 3 ORIGIN FOR THE GROUP (A): 28.9143 36.1562 13.122 REMARK 3 T TENSOR REMARK 3 T11: 0.1688 T22: -0.1377 REMARK 3 T33: 0.0034 T12: 0.2101 REMARK 3 T13: 0.0651 T23: -0.0892 REMARK 3 L TENSOR REMARK 3 L11: 8.9803 L22: 0.2366 REMARK 3 L33: 16.6309 L12: -2.8462 REMARK 3 L13: 4.369 L23: 2.1288 REMARK 3 S TENSOR REMARK 3 S11: -0.1601 S12: 0.1262 S13: -1.025 REMARK 3 S21: 0.1262 S22: 0.4845 S23: 0.0569 REMARK 3 S31: -1.025 S32: 0.0569 S33: -0.3244 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: { C|849 - C|859 } REMARK 3 ORIGIN FOR THE GROUP (A): 23.8347 28.4933 -7.8124 REMARK 3 T TENSOR REMARK 3 T11: 0.2762 T22: 0.2459 REMARK 3 T33: -0.1261 T12: 0.2052 REMARK 3 T13: 0.1333 T23: -0.0512 REMARK 3 L TENSOR REMARK 3 L11: 0 L22: 4.1132 REMARK 3 L33: 16.6309 L12: -5.8208 REMARK 3 L13: -5.43 L23: 2.3002 REMARK 3 S TENSOR REMARK 3 S11: -0.1703 S12: 0.0573 S13: -0.3575 REMARK 3 S21: 0.0573 S22: 0.3407 S23: -0.633 REMARK 3 S31: -0.3575 S32: -0.633 S33: -0.1703 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: { C|1002 - C|1002 } REMARK 3 ORIGIN FOR THE GROUP (A): 29.4192 39.6751 12.11 REMARK 3 T TENSOR REMARK 3 T11: 0.046 T22: 0.0665 REMARK 3 T33: 0.1773 T12: 0.2112 REMARK 3 T13: 0.1166 T23: -0.0645 REMARK 3 L TENSOR REMARK 3 L11: 3.3178 L22: 3.7052 REMARK 3 L33: 10.9851 L12: -4.8419 REMARK 3 L13: 2.2315 L23: -0.4166 REMARK 3 S TENSOR REMARK 3 S11: 0.5264 S12: 0.1064 S13: -0.3611 REMARK 3 S21: 0.1064 S22: -0.0305 S23: 0.0471 REMARK 3 S31: -0.3611 S32: 0.0471 S33: -0.4959 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINED USING LOCAL NCS RESTRAINTS PLUS REMARK 3 ADDITIONAL RESTRAINTS FOR THE ZINC ATOMS TO ENFORCE CHEMICALLY REMARK 3 PLAUSIBLE COORDINATION. REMARK 4 REMARK 4 6ZE9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109241. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 1.28096 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 0.5.902-GFFA11588-DIALS REMARK 200 -1.14 REMARK 200 DATA SCALING SOFTWARE : XIA2 0.5.902-GFFA11588-DIALS REMARK 200 -1.14 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5148 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 1.17800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CRANK2 2.0.229 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES PH 7.5, 200 MM AMMONIUM REMARK 280 ACETATE, 45% (V/V) 2-METHYL-2,4-PENTANEDIOL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z+1/2 REMARK 290 4555 Y,-X,Z+1/2 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z+1/2 REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.71150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.71150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 19.71150 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 19.71150 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -177.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 19.71150 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -163.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 104.17800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 39.42300 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 104.17800 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 39.42300 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 MET A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 MET B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 MET C -7 REMARK 465 HIS C -6 REMARK 465 HIS C -5 REMARK 465 HIS C -4 REMARK 465 VAL C 870 REMARK 465 ASN C 871 REMARK 465 PRO C 872 REMARK 465 ALA C 873 REMARK 465 ASP C 874 REMARK 465 THR C 875 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 C 858 54.86 -145.38 REMARK 500 SER C 867 -87.09 -111.19 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 A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A -3 NE2 REMARK 620 2 HIS A -1 NE2 105.7 REMARK 620 3 THR B 875 O 118.8 107.6 REMARK 620 4 CYS C 844 SG 110.8 116.1 98.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 844 SG REMARK 620 2 HIS C -3 NE2 112.5 REMARK 620 3 HIS C -1 NE2 108.3 109.5 REMARK 620 4 HOH C1101 O 110.9 107.0 108.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 875 O REMARK 620 2 HIS B -3 NE2 108.9 REMARK 620 3 HIS B -1 NE2 112.1 96.9 REMARK 620 4 CYS B 844 SG 128.5 122.5 68.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 1001 DBREF 6ZE9 A 840 875 UNP Q96JC1 VPS39_HUMAN 840 875 DBREF 6ZE9 B 840 875 UNP Q96JC1 VPS39_HUMAN 840 875 DBREF 6ZE9 C 840 875 UNP Q96JC1 VPS39_HUMAN 840 875 SEQADV 6ZE9 MET A -7 UNP Q96JC1 INITIATING METHIONINE SEQADV 6ZE9 HIS A -6 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS A -5 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS A -4 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS A -3 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS A -2 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS A -1 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 MET A 0 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 MET B -7 UNP Q96JC1 INITIATING METHIONINE SEQADV 6ZE9 HIS B -6 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS B -5 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS B -4 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS B -3 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS B -2 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS B -1 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 MET B 0 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 MET C -7 UNP Q96JC1 INITIATING METHIONINE SEQADV 6ZE9 HIS C -6 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS C -5 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS C -4 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS C -3 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS C -2 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 HIS C -1 UNP Q96JC1 EXPRESSION TAG SEQADV 6ZE9 MET C 0 UNP Q96JC1 EXPRESSION TAG SEQRES 1 A 44 MET HIS HIS HIS HIS HIS HIS MET VAL CYS MET VAL CYS SEQRES 2 A 44 LYS LYS LYS ILE GLY ASN SER ALA PHE ALA ARG TYR PRO SEQRES 3 A 44 ASN GLY VAL VAL VAL HIS TYR PHE CYS SER LYS GLU VAL SEQRES 4 A 44 ASN PRO ALA ASP THR SEQRES 1 B 44 MET HIS HIS HIS HIS HIS HIS MET VAL CYS MET VAL CYS SEQRES 2 B 44 LYS LYS LYS ILE GLY ASN SER ALA PHE ALA ARG TYR PRO SEQRES 3 B 44 ASN GLY VAL VAL VAL HIS TYR PHE CYS SER LYS GLU VAL SEQRES 4 B 44 ASN PRO ALA ASP THR SEQRES 1 C 44 MET HIS HIS HIS HIS HIS HIS MET VAL CYS MET VAL CYS SEQRES 2 C 44 LYS LYS LYS ILE GLY ASN SER ALA PHE ALA ARG TYR PRO SEQRES 3 C 44 ASN GLY VAL VAL VAL HIS TYR PHE CYS SER LYS GLU VAL SEQRES 4 C 44 ASN PRO ALA ASP THR HET ZN A1001 1 HET ZN B1001 1 HET ZN C1001 1 HETNAM ZN ZINC ION FORMUL 4 ZN 3(ZN 2+) FORMUL 7 HOH *(H2 O) HELIX 1 AA1 ASN A 871 THR A 875 5 5 HELIX 2 AA2 ASN B 871 THR B 875 5 5 SHEET 1 AA1 4 VAL A 860 CYS A 866 0 SHEET 2 AA1 4 HIS A -3 LYS A 847 -1 N MET A 842 O PHE A 865 SHEET 3 AA1 4 HIS C -2 LYS C 847 -1 O MET C 0 N VAL A 843 SHEET 4 AA1 4 VAL C 860 CYS C 866 -1 O VAL C 861 N LYS C 846 SHEET 1 AA2 2 CYS B 841 LYS B 847 0 SHEET 2 AA2 2 VAL B 860 CYS B 866 -1 O PHE B 865 N MET B 842 SSBOND 1 CYS A 841 CYS A 866 1555 1555 2.03 SSBOND 2 CYS B 841 CYS B 866 1555 1555 2.04 SSBOND 3 CYS C 841 CYS C 866 1555 1555 2.04 LINK NE2 HIS A -3 ZN ZN A1001 1555 1555 1.99 LINK NE2 HIS A -1 ZN ZN A1001 1555 1555 2.15 LINK SG CYS A 844 ZN ZN C1001 1555 1555 2.29 LINK O THR A 875 ZN ZN B1001 1555 1555 1.93 LINK ZN ZN A1001 O THR B 875 1555 1555 2.06 LINK ZN ZN A1001 SG CYS C 844 1555 1555 2.28 LINK NE2 HIS B -3 ZN ZN B1001 1555 1555 2.08 LINK NE2 HIS B -1 ZN ZN B1001 1555 1555 1.99 LINK SG CYS B 844 ZN ZN B1001 1555 6566 2.29 LINK NE2 HIS C -3 ZN ZN C1001 1555 1555 2.10 LINK NE2 HIS C -1 ZN ZN C1001 1555 1555 2.02 LINK ZN ZN C1001 O HOH C1101 1555 1555 2.32 SITE 1 AC1 4 HIS A -3 HIS A -1 THR B 875 CYS C 844 SITE 1 AC2 4 THR A 875 HIS B -3 HIS B -1 CYS B 844 SITE 1 AC3 4 CYS A 844 HIS C -1 HIS C -3 HOH C1101 CRYST1 104.178 104.178 39.423 90.00 90.00 90.00 P 42 2 2 24 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 0.009599 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025366 0.00000