PDB Short entry for 4AFI HEADER ENDOCYTOSIS 19-JAN-12 4AFI TITLE COMPLEX BETWEEN VAMP7 LONGIN DOMAIN AND FRAGMENT OF DELTA-ADAPTIN FROM TITLE 2 AP3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AP-3 COMPLEX SUBUNIT DELTA-1, VESICLE-ASSOCIATED MEMBRANE COMPND 3 PROTEIN 7; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: DELTA-ADAPTIN HINGE, RESIDUES 680-729, VAMP7 LONGIN DOMAIN, COMPND 6 RESIDUES 1-120; COMPND 7 SYNONYM: AP-3 COMPLEX SUBUNIT DELTA, ADAPTER-RELATED PROTEIN COMPLEX COMPND 8 3 SUBUNIT DELTA-1, DELTA-ADAPTIN, VAMP-7, SYNAPTOBREVIN-LIKE PROTEIN COMPND 9 1; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HUMAN, HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 9606, 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T2 KEYWDS ENDOCYTOSIS, EXOCYTOSIS, CLATHRIN ADAPTOR, CHIMERA, FUSION PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.M.KENT,P.R.EVANS,J.P.LUZIO,A.A.PEDEN,D.J.OWEN REVDAT 4 20-DEC-23 4AFI 1 REMARK LINK REVDAT 3 15-MAR-17 4AFI 1 SOURCE REVDAT 2 22-AUG-12 4AFI 1 JRNL REVDAT 1 30-MAY-12 4AFI 0 JRNL AUTH H.M.KENT,P.R.EVANS,I.B.SCHAEFER,S.R.GRAY,C.M.SANDERSON, JRNL AUTH 2 J.P.LUZIO,A.A.PEDEN,D.J.OWEN JRNL TITL STRUCTURAL BASIS OF THE INTRACELLULAR SORTING OF THE SNARE JRNL TITL 2 VAMP7 BY THE AP3 ADAPTOR COMPLEX JRNL REF DEV.CELL V. 22 979 2012 JRNL REFN ISSN 1534-5807 JRNL PMID 22521722 JRNL DOI 10.1016/J.DEVCEL.2012.01.018 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0002 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11194 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) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 551 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 683 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.4570 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.4400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2439 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.27000 REMARK 3 B22 (A**2) : 4.27000 REMARK 3 B33 (A**2) : -8.55000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.863 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.336 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.316 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.216 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2496 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1662 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3387 ; 1.566 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4060 ; 1.189 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 305 ; 6.612 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;36.888 ;24.087 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 420 ;18.506 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;17.412 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 382 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2764 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 512 ; 0.004 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 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. U VALUES REFINED INDIVIDUALLY. NCS APPLIED AS LOCAL REMARK 3 RESTRAINTS WITH ADDITIONAL TARGET OF PREVIOUS VAMP7 STRUCTURE. REMARK 4 REMARK 4 4AFI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1290050995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11810 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 64.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.31000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.60 REMARK 200 R MERGE FOR SHELL (I) : 2.90000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 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: PDB ENTRY 2VX8 REMARK 200 REMARK 200 REMARK: SIGNIFICANT ANISOTROPY IN DATA. SECOND DATA SET AT 1.5 REMARK 200 ANGSTROM UNITS. COLLECTED TO ENHANCE ANOMALOUS DATA FROM PR3+ REMARK 200 IONS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4 M NACL, 100 MM BICINE PH 9.0, 10 MM REMARK 280 PRASEODYMIUM ACETATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z 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 108.95750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.77750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.77750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 163.43625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.77750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.77750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.47875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.77750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.77750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 163.43625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.77750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.77750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.47875 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 0.00000 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 108.95750 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: 5730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 PRO A 3 REMARK 465 PHE A 4 REMARK 465 TYR A 5 REMARK 465 ILE A 6 REMARK 465 LYS A 7 REMARK 465 SER A 8 REMARK 465 SER A 9 REMARK 465 PRO A 10 REMARK 465 SER A 11 REMARK 465 PRO A 12 REMARK 465 GLN A 13 REMARK 465 LYS A 14 REMARK 465 ARG A 15 REMARK 465 TYR A 16 REMARK 465 GLN A 17 REMARK 465 ASP A 18 REMARK 465 GLY B 1 REMARK 465 SER B 2 REMARK 465 PRO B 3 REMARK 465 PHE B 4 REMARK 465 TYR B 5 REMARK 465 ILE B 6 REMARK 465 LYS B 7 REMARK 465 SER B 8 REMARK 465 SER B 9 REMARK 465 PRO B 10 REMARK 465 SER B 11 REMARK 465 PRO B 12 REMARK 465 GLN B 13 REMARK 465 LYS B 14 REMARK 465 ARG B 15 REMARK 465 TYR B 16 REMARK 465 GLN B 17 REMARK 465 ASP B 18 REMARK 465 THR B 19 REMARK 465 PRO B 20 REMARK 465 ASN B 173 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 PRO A 20 -169.35 -71.69 REMARK 500 PRO A 42 72.84 -100.37 REMARK 500 MET A 43 -59.86 177.40 REMARK 500 ALA A 55 -112.73 -117.94 REMARK 500 ASN A 94 -177.93 177.47 REMARK 500 ARG A 112 -11.71 67.74 REMARK 500 TYR A 153 14.06 53.60 REMARK 500 VAL B 22 20.13 -140.50 REMARK 500 GLU B 51 77.30 -65.71 REMARK 500 ARG B 112 -12.87 68.19 REMARK 500 TYR B 153 10.57 55.01 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 PR A1000 PR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 120 OD1 REMARK 620 2 ASP A 120 OD2 40.9 REMARK 620 3 ASP A 121 OD1 68.7 102.2 REMARK 620 4 ASP A 122 OD2 82.4 63.7 82.1 REMARK 620 5 HOH A2001 O 84.7 51.0 152.6 88.4 REMARK 620 6 HOH A2002 O 121.4 112.7 132.9 141.3 66.5 REMARK 620 7 ASP B 45 OD2 153.1 152.8 84.6 91.7 121.5 78.6 REMARK 620 8 ASP B 45 OD1 146.4 105.6 138.2 82.9 64.9 60.3 57.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PR B1000 PR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 52 OE2 REMARK 620 2 ASP B 120 OD1 74.8 REMARK 620 3 ASP B 120 OD2 55.5 38.6 REMARK 620 4 ASP B 121 OD1 123.2 58.4 67.8 REMARK 620 5 ASP B 122 OD2 90.9 102.8 70.8 71.9 REMARK 620 6 HOH B2001 O 76.9 136.8 132.2 159.8 109.6 REMARK 620 7 HOH B2002 O 143.0 112.4 148.9 87.5 120.5 74.3 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PR A 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PR B 1000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VX8 RELATED DB: PDB REMARK 900 VAMP7 LONGIN DOMAIN HRB PEPTIDE COMPLEX DBREF 4AFI A 3 52 UNP O14617 AP3D1_HUMAN 680 729 DBREF 4AFI A 54 173 UNP P70280 VAMP7_MOUSE 1 120 DBREF 4AFI B 3 52 UNP O14617 AP3D1_HUMAN 680 729 DBREF 4AFI B 54 173 UNP P70280 VAMP7_MOUSE 1 120 SEQADV 4AFI GLY A 1 UNP P70280 EXPRESSION TAG SEQADV 4AFI SER A 2 UNP P70280 EXPRESSION TAG SEQADV 4AFI GLY B 1 UNP P70280 EXPRESSION TAG SEQADV 4AFI SER B 2 UNP P70280 EXPRESSION TAG SEQRES 1 A 173 GLY SER PRO PHE TYR ILE LYS SER SER PRO SER PRO GLN SEQRES 2 A 173 LYS ARG TYR GLN ASP THR PRO GLY VAL GLU HIS ILE PRO SEQRES 3 A 173 VAL VAL GLN ILE ASP LEU SER VAL PRO LEU LYS VAL PRO SEQRES 4 A 173 GLY LEU PRO MET SER ASP GLN TYR VAL LYS LEU GLU GLU SEQRES 5 A 173 ALA MET ALA ILE LEU PHE ALA VAL VAL ALA ARG GLY THR SEQRES 6 A 173 THR ILE LEU ALA LYS HIS ALA TRP CYS GLY GLY ASN PHE SEQRES 7 A 173 LEU GLU VAL THR GLU GLN ILE LEU ALA LYS ILE PRO SER SEQRES 8 A 173 GLU ASN ASN LYS LEU THR TYR SER HIS GLY ASN TYR LEU SEQRES 9 A 173 PHE HIS TYR ILE CYS GLN ASP ARG ILE VAL TYR LEU CYS SEQRES 10 A 173 ILE THR ASP ASP ASP PHE GLU ARG SER ARG ALA PHE SER SEQRES 11 A 173 PHE LEU ASN GLU VAL LYS LYS ARG PHE GLN THR THR TYR SEQRES 12 A 173 GLY SER ARG ALA GLN THR ALA LEU PRO TYR ALA MET ASN SEQRES 13 A 173 SER GLU PHE SER SER VAL LEU ALA ALA GLN LEU LYS HIS SEQRES 14 A 173 HIS SER GLU ASN SEQRES 1 B 173 GLY SER PRO PHE TYR ILE LYS SER SER PRO SER PRO GLN SEQRES 2 B 173 LYS ARG TYR GLN ASP THR PRO GLY VAL GLU HIS ILE PRO SEQRES 3 B 173 VAL VAL GLN ILE ASP LEU SER VAL PRO LEU LYS VAL PRO SEQRES 4 B 173 GLY LEU PRO MET SER ASP GLN TYR VAL LYS LEU GLU GLU SEQRES 5 B 173 ALA MET ALA ILE LEU PHE ALA VAL VAL ALA ARG GLY THR SEQRES 6 B 173 THR ILE LEU ALA LYS HIS ALA TRP CYS GLY GLY ASN PHE SEQRES 7 B 173 LEU GLU VAL THR GLU GLN ILE LEU ALA LYS ILE PRO SER SEQRES 8 B 173 GLU ASN ASN LYS LEU THR TYR SER HIS GLY ASN TYR LEU SEQRES 9 B 173 PHE HIS TYR ILE CYS GLN ASP ARG ILE VAL TYR LEU CYS SEQRES 10 B 173 ILE THR ASP ASP ASP PHE GLU ARG SER ARG ALA PHE SER SEQRES 11 B 173 PHE LEU ASN GLU VAL LYS LYS ARG PHE GLN THR THR TYR SEQRES 12 B 173 GLY SER ARG ALA GLN THR ALA LEU PRO TYR ALA MET ASN SEQRES 13 B 173 SER GLU PHE SER SER VAL LEU ALA ALA GLN LEU LYS HIS SEQRES 14 B 173 HIS SER GLU ASN HET PR A1000 1 HET PR B1000 1 HETNAM PR PRASEODYMIUM ION FORMUL 3 PR 2(PR 3+) FORMUL 5 HOH *4(H2 O) HELIX 1 1 ASN A 77 ALA A 87 1 11 HELIX 2 2 GLU A 124 GLY A 144 1 21 HELIX 3 3 SER A 145 THR A 149 5 5 HELIX 4 4 MET A 155 ASN A 173 1 19 HELIX 5 5 ASN B 77 ALA B 87 1 11 HELIX 6 6 GLU B 124 GLY B 144 1 21 HELIX 7 7 SER B 145 THR B 149 5 5 HELIX 8 8 MET B 155 GLU B 172 1 18 SHEET 1 AA 6 VAL A 27 GLN A 29 0 SHEET 2 AA 6 ASN B 94 HIS B 100 1 O THR B 97 N VAL A 28 SHEET 3 AA 6 TYR B 103 GLN B 110 -1 O TYR B 103 N HIS B 100 SHEET 4 AA 6 ILE B 113 ASP B 120 -1 O ILE B 113 N GLN B 110 SHEET 5 AA 6 ILE B 56 ARG B 63 -1 N LEU B 57 O ILE B 118 SHEET 6 AA 6 THR B 66 ALA B 72 -1 O THR B 66 N ARG B 63 SHEET 1 AB 2 TYR A 47 LYS A 49 0 SHEET 2 AB 2 TYR B 47 LYS B 49 -1 O VAL B 48 N VAL A 48 SHEET 1 AC 6 THR A 66 ALA A 72 0 SHEET 2 AC 6 ILE A 56 ARG A 63 -1 O ALA A 59 N HIS A 71 SHEET 3 AC 6 ILE A 113 ASP A 120 -1 O VAL A 114 N ALA A 62 SHEET 4 AC 6 TYR A 103 GLN A 110 -1 O LEU A 104 N THR A 119 SHEET 5 AC 6 ASN A 94 HIS A 100 -1 O ASN A 94 N CYS A 109 SHEET 6 AC 6 VAL B 27 GLN B 29 1 O VAL B 28 N SER A 99 LINK OD1 ASP A 120 PR PR A1000 1555 1555 2.10 LINK OD2 ASP A 120 PR PR A1000 1555 1555 3.23 LINK OD1 ASP A 121 PR PR A1000 1555 1555 2.12 LINK OD2 ASP A 122 PR PR A1000 1555 1555 2.12 LINK PR PR A1000 O HOH A2001 1555 1555 2.77 LINK PR PR A1000 O HOH A2002 1555 1555 2.53 LINK PR PR A1000 OD2 ASP B 45 1555 1555 2.29 LINK PR PR A1000 OD1 ASP B 45 1555 1555 2.28 LINK OE2 GLU B 52 PR PR B1000 1555 1555 2.18 LINK OD1 ASP B 120 PR PR B1000 1555 1555 3.48 LINK OD2 ASP B 120 PR PR B1000 1555 1555 2.95 LINK OD1 ASP B 121 PR PR B1000 1555 1555 2.57 LINK OD2 ASP B 122 PR PR B1000 1555 1555 2.08 LINK PR PR B1000 O HOH B2001 1555 1555 2.62 LINK PR PR B1000 O HOH B2002 1555 1555 2.50 SITE 1 AC1 6 ASP A 120 ASP A 121 ASP A 122 HOH A2001 SITE 2 AC1 6 HOH A2002 ASP B 45 SITE 1 AC2 6 GLU B 52 ASP B 120 ASP B 121 ASP B 122 SITE 2 AC2 6 HOH B2001 HOH B2002 CRYST1 63.555 63.555 217.915 90.00 90.00 90.00 P 43 21 2 16 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 0.015734 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015734 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004589 0.00000 MTRIX1 1 -0.766000 0.632000 0.120000 62.34500 1 MTRIX2 1 -0.639000 -0.768000 -0.042000 -68.14300 1 MTRIX3 1 0.066000 -0.109000 0.992000 13.24500 1