HEADER PROTEIN TRANSPORT 22-FEB-10 3LVR TITLE THE CRYSTAL STRUCTURE OF ASAP3 IN COMPLEX WITH ARF6 IN TRANSITION TITLE 2 STATE SOAKED WITH CALCIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARF-GAP WITH SH3 DOMAIN, ANK REPEAT AND PH DOMAIN- COMPND 3 CONTAINING PROTEIN 3, ADP-RIBOSYLATION FACTOR 6; COMPND 4 CHAIN: E; COMPND 5 FRAGMENT: GAP AND ANKYRIN DOMAIN, RESIDUES 416-697, RESIDUES 11-175; COMPND 6 SYNONYM: ASAP3, DEVELOPMENT AND DIFFERENTIATION-ENHANCING FACTOR-LIKE COMPND 7 1, PROTEIN UP-REGULATED IN LIVER CANCER 1, ARF6, UPLC1; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: MISSING THE N-TERMINUS AMPHIPATHIC HELIX FOR ARF6 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606, 32630; SOURCE 5 GENE: ASAP3, ARF6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARF6, ASAP3, UPLC1, GDP, CALCIUM, ARFGAP, ARF, LINKERS, ALTERNATIVE KEYWDS 2 SPLICING, ANK REPEAT, COILED COIL, CYTOPLASM, METAL-BINDING, KEYWDS 3 PHOSPHOPROTEIN, POLYMORPHISM, ZINC, ZINC-FINGER, CELL MEMBRANE, KEYWDS 4 ENDOSOME, ER-GOLGI TRANSPORT, GOLGI APPARATUS, GTP-BINDING, KEYWDS 5 LIPOPROTEIN, MYRISTATE, NUCLEOTIDE-BINDING, PROTEIN TRANSPORT, KEYWDS 6 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.A.ISMAIL,I.R.VETTER,B.SOT,A.WITTINGHOFER REVDAT 5 01-NOV-23 3LVR 1 REMARK SEQADV LINK REVDAT 4 08-NOV-17 3LVR 1 REMARK REVDAT 3 09-AUG-17 3LVR 1 SOURCE REMARK REVDAT 2 16-JUN-10 3LVR 1 JRNL REVDAT 1 09-JUN-10 3LVR 0 JRNL AUTH S.A.ISMAIL,I.R.VETTER,B.SOT,A.WITTINGHOFER JRNL TITL THE STRUCTURE OF AN ARF-ARFGAP COMPLEX REVEALS A CA2+ JRNL TITL 2 REGULATORY MECHANISM JRNL REF CELL(CAMBRIDGE,MASS.) V. 141 812 2010 JRNL REFN ISSN 0092-8674 JRNL PMID 20510928 JRNL DOI 10.1016/J.CELL.2010.03.051 REMARK 2 REMARK 2 RESOLUTION. 3.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 3.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 8294 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 437 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) : 3.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 601 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 32 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3257 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 125.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.75000 REMARK 3 B22 (A**2) : -6.75000 REMARK 3 B33 (A**2) : 10.13000 REMARK 3 B12 (A**2) : -3.38000 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): 0.610 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.451 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 56.231 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3348 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4540 ; 1.058 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 415 ; 5.473 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;38.465 ;24.211 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 575 ;17.901 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;13.860 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 513 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2509 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1544 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2257 ; 0.299 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 114 ; 0.137 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.113 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 27 ; 0.195 ; 0.200 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): 2129 ; 0.223 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3329 ; 0.405 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1375 ; 0.446 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1211 ; 0.813 ; 4.500 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 423 E 679 REMARK 3 ORIGIN FOR THE GROUP (A): 37.7090 31.5561 -3.2190 REMARK 3 T TENSOR REMARK 3 T11: -0.5114 T22: -0.3132 REMARK 3 T33: -0.4966 T12: 0.1040 REMARK 3 T13: 0.1519 T23: -0.1904 REMARK 3 L TENSOR REMARK 3 L11: 5.3368 L22: 9.7407 REMARK 3 L33: 4.9919 L12: 1.1971 REMARK 3 L13: -0.0031 L23: -0.8969 REMARK 3 S TENSOR REMARK 3 S11: -0.1094 S12: 0.0863 S13: -0.7944 REMARK 3 S21: 0.0645 S22: 0.1212 S23: -0.4716 REMARK 3 S31: 0.7445 S32: -0.4123 S33: -0.0118 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 11 A 174 REMARK 3 ORIGIN FOR THE GROUP (A): 20.5949 55.7745 5.3018 REMARK 3 T TENSOR REMARK 3 T11: -0.7100 T22: -0.6942 REMARK 3 T33: -0.4774 T12: 0.0865 REMARK 3 T13: 0.1309 T23: -0.1082 REMARK 3 L TENSOR REMARK 3 L11: 11.3975 L22: 7.8783 REMARK 3 L33: 5.7939 L12: 0.2885 REMARK 3 L13: 0.3194 L23: 0.0237 REMARK 3 S TENSOR REMARK 3 S11: -0.2783 S12: -0.3039 S13: 0.8954 REMARK 3 S21: 0.3346 S22: 0.0096 S23: 0.8382 REMARK 3 S31: -0.1207 S32: -0.2749 S33: 0.2687 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 3LVR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000057790. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-09 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 : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3838 REMARK 200 MONOCHROMATOR : SAGITALLY - HORIZONTALLY FOCUSED REMARK 200 SI(111) MONOCHROMATOR REMARK 200 OPTICS : NULL 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8310 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.380 REMARK 200 RESOLUTION RANGE LOW (A) : 29.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.850 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.57500 REMARK 200 R SYM FOR SHELL (I) : 0.67600 REMARK 200 FOR SHELL : 3.500 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: PDB ENTRY 3LVQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG 8000, 150MM MAGNESIUM ACETATE, REMARK 280 100MM MOPS(PH 7.5); CRYSTALS WERE THEN SOAKED IN 30MM CACL2 , REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 33.08000 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 16.54000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.08000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.54000 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: 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 E 416 REMARK 465 HIS E 417 REMARK 465 ASP E 418 REMARK 465 GLY E 419 REMARK 465 GLU E 420 REMARK 465 PRO E 421 REMARK 465 HIS E 422 REMARK 465 PRO E 546 REMARK 465 ALA E 620 REMARK 465 GLY E 680 REMARK 465 THR E 681 REMARK 465 PHE E 682 REMARK 465 ALA E 683 REMARK 465 PHE E 684 REMARK 465 PRO E 685 REMARK 465 LEU E 686 REMARK 465 HIS E 687 REMARK 465 VAL E 688 REMARK 465 ASP E 689 REMARK 465 TYR E 690 REMARK 465 SER E 691 REMARK 465 TRP E 692 REMARK 465 VAL E 693 REMARK 465 ILE E 694 REMARK 465 SER E 695 REMARK 465 THR E 696 REMARK 465 GLU E 697 REMARK 465 ASN E 698 REMARK 465 LEU E 699 REMARK 465 SER E 700 REMARK 465 SER E 701 REMARK 465 ASP E 702 REMARK 465 SER E 703 REMARK 465 SER E 704 REMARK 465 LEU E 705 REMARK 465 SER E 706 REMARK 465 SER E 707 REMARK 465 PRO E 708 REMARK 465 SER E 709 REMARK 465 ALA E 710 REMARK 465 LEU E 711 REMARK 465 ASN E 712 REMARK 465 SER E 713 REMARK 465 LEU E 714 REMARK 465 SER E 715 REMARK 465 SER E 716 REMARK 465 PRO E 717 REMARK 465 SER E 718 REMARK 465 ALA E 719 REMARK 465 LEU E 720 REMARK 465 ASN E 721 REMARK 465 SER E 722 REMARK 465 THR E 723 REMARK 465 ALA E 724 REMARK 465 SER E 725 REMARK 465 ASN E 726 REMARK 465 SER E 727 REMARK 465 PRO E 728 REMARK 465 GLY E 729 REMARK 465 ILE E 730 REMARK 465 GLU E 731 REMARK 465 GLY E 732 REMARK 465 LEU E 733 REMARK 465 SER E 734 REMARK 465 SER E 175 REMARK 465 LYS E 176 REMARK 465 LEU E 177 REMARK 465 ALA E 178 REMARK 465 ALA E 179 REMARK 465 ALA E 180 REMARK 465 LEU E 181 REMARK 465 GLU E 182 REMARK 465 HIS E 183 REMARK 465 HIS E 184 REMARK 465 HIS E 185 REMARK 465 HIS E 186 REMARK 465 HIS E 187 REMARK 465 HIS E 188 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 ASP E 606 CG OD1 OD2 REMARK 470 ASN E 11 CG OD1 ND2 REMARK 470 LYS E 12 CG CD CE NZ REMARK 470 GLU E 13 CG CD OE1 OE2 REMARK 470 LYS E 174 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 O3B GDP E 737 AL AF3 E 738 1.80 REMARK 500 AL AF3 E 738 O HOH E 230 1.97 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 ASP E 448 96.94 -14.51 REMARK 500 MET E 497 -87.21 -129.73 REMARK 500 GLN E 509 43.80 -92.44 REMARK 500 ALA E 520 -76.30 -15.22 REMARK 500 CYS E 544 -172.70 -177.10 REMARK 500 ASP E 572 92.91 66.16 REMARK 500 PRO E 580 -147.16 -71.52 REMARK 500 VAL E 596 45.82 -100.61 REMARK 500 LYS E 618 -69.20 -121.76 REMARK 500 ASN E 633 70.84 55.85 REMARK 500 GLN E 634 76.02 -119.14 REMARK 500 ARG E 645 88.17 54.61 REMARK 500 ASN E 652 -157.10 -110.73 REMARK 500 LYS E 12 75.43 43.55 REMARK 500 THR E 53 67.73 -112.48 REMARK 500 PRO E 72 -5.49 -56.91 REMARK 500 ARG E 95 48.89 -106.36 REMARK 500 MET E 112 5.80 -151.30 REMARK 500 ASP E 114 42.16 -72.55 REMARK 500 PRO E 127 -86.96 -47.28 REMARK 500 MET E 130 106.63 71.83 REMARK 500 LEU E 139 0.14 -67.87 REMARK 500 TYR E 150 111.02 -167.02 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 MG E 736 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR E 27 OG1 REMARK 620 2 THR E 44 OG1 78.3 REMARK 620 3 HOH E 220 O 57.8 73.9 REMARK 620 4 GDP E 737 O2B 73.4 137.9 64.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E 739 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP E 68 OD2 REMARK 620 2 ASP E 68 OD1 45.7 REMARK 620 3 GLU E 98 OE2 115.8 70.1 REMARK 620 4 HOH E 232 O 80.1 87.2 99.0 REMARK 620 5 GLN E 479 OE1 79.3 124.0 161.8 93.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 735 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 441 SG REMARK 620 2 CYS E 444 SG 119.0 REMARK 620 3 CYS E 461 SG 114.1 112.0 REMARK 620 4 CYS E 464 SG 100.0 103.0 106.4 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 E 735 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 736 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP E 737 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AF3 E 738 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 739 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LVQ RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEX IN TRANSITION STATE REMARK 999 REMARK 999 SEQUENCE REMARK 999 NLSSDSSLSSPSALNSLSSPSALNSTASNSPGIEGLS IS A FLEXIBLE LINKER REGION. REMARK 999 THIS ENTRY USES NON-SEQUENTIAL NUMBERING. DBREF 3LVR E 416 697 UNP Q8TDY4 ASAP3_HUMAN 416 697 DBREF 3LVR E 698 734 PDB 3LVQ 3LVQ 698 734 DBREF 3LVR E 11 175 UNP P62330 ARF6_HUMAN 11 175 SEQADV 3LVR LYS E 176 UNP P62330 EXPRESSION TAG SEQADV 3LVR LEU E 177 UNP P62330 EXPRESSION TAG SEQADV 3LVR ALA E 178 UNP P62330 EXPRESSION TAG SEQADV 3LVR ALA E 179 UNP P62330 EXPRESSION TAG SEQADV 3LVR ALA E 180 UNP P62330 EXPRESSION TAG SEQADV 3LVR LEU E 181 UNP P62330 EXPRESSION TAG SEQADV 3LVR GLU E 182 UNP P62330 EXPRESSION TAG SEQADV 3LVR HIS E 183 UNP P62330 EXPRESSION TAG SEQADV 3LVR HIS E 184 UNP P62330 EXPRESSION TAG SEQADV 3LVR HIS E 185 UNP P62330 EXPRESSION TAG SEQADV 3LVR HIS E 186 UNP P62330 EXPRESSION TAG SEQADV 3LVR HIS E 187 UNP P62330 EXPRESSION TAG SEQADV 3LVR HIS E 188 UNP P62330 EXPRESSION TAG SEQRES 1 E 497 GLY HIS ASP GLY GLU PRO HIS ASP LEU THR LYS LEU LEU SEQRES 2 E 497 ILE ALA GLU VAL LYS SER ARG PRO GLY ASN SER GLN CYS SEQRES 3 E 497 CYS ASP CYS GLY ALA ALA ASP PRO THR TRP LEU SER THR SEQRES 4 E 497 ASN LEU GLY VAL LEU THR CYS ILE GLN CYS SER GLY VAL SEQRES 5 E 497 HIS ARG GLU LEU GLY VAL ARG PHE SER ARG MET GLN SER SEQRES 6 E 497 LEU THR LEU ASP LEU LEU GLY PRO SER GLU LEU LEU LEU SEQRES 7 E 497 ALA LEU ASN MET GLY ASN THR SER PHE ASN GLU VAL MET SEQRES 8 E 497 GLU ALA GLN LEU PRO SER HIS GLY GLY PRO LYS PRO SER SEQRES 9 E 497 ALA GLU SER ASP MET GLY THR ARG ARG ASP TYR ILE MET SEQRES 10 E 497 ALA LYS TYR VAL GLU HIS ARG PHE ALA ARG ARG CYS THR SEQRES 11 E 497 PRO GLU PRO GLN ARG LEU TRP THR ALA ILE CYS ASN ARG SEQRES 12 E 497 ASP LEU LEU SER VAL LEU GLU ALA PHE ALA ASN GLY GLN SEQRES 13 E 497 ASP PHE GLY GLN PRO LEU PRO GLY PRO ASP ALA GLN ALA SEQRES 14 E 497 PRO GLU GLU LEU VAL LEU HIS LEU ALA VAL LYS VAL ALA SEQRES 15 E 497 ASN GLN ALA SER LEU PRO LEU VAL ASP PHE ILE ILE GLN SEQRES 16 E 497 ASN GLY GLY HIS LEU ASP ALA LYS ALA ALA ASP GLY ASN SEQRES 17 E 497 THR ALA LEU HIS TYR ALA ALA LEU TYR ASN GLN PRO ASP SEQRES 18 E 497 CYS LEU LYS LEU LEU LEU LYS GLY ARG ALA LEU VAL GLY SEQRES 19 E 497 THR VAL ASN GLU ALA GLY GLU THR ALA LEU ASP ILE ALA SEQRES 20 E 497 ARG LYS LYS HIS HIS LYS GLU CYS GLU GLU LEU LEU GLU SEQRES 21 E 497 GLN ALA GLN ALA GLY THR PHE ALA PHE PRO LEU HIS VAL SEQRES 22 E 497 ASP TYR SER TRP VAL ILE SER THR GLU ASN LEU SER SER SEQRES 23 E 497 ASP SER SER LEU SER SER PRO SER ALA LEU ASN SER LEU SEQRES 24 E 497 SER SER PRO SER ALA LEU ASN SER THR ALA SER ASN SER SEQRES 25 E 497 PRO GLY ILE GLU GLY LEU SER ASN LYS GLU MET ARG ILE SEQRES 26 E 497 LEU MET LEU GLY LEU ASP ALA ALA GLY LYS THR THR ILE SEQRES 27 E 497 LEU TYR LYS LEU LYS LEU GLY GLN SER VAL THR THR ILE SEQRES 28 E 497 PRO THR VAL GLY PHE ASN VAL GLU THR VAL THR TYR LYS SEQRES 29 E 497 ASN VAL LYS PHE ASN VAL TRP ASP VAL GLY GLY GLN ASP SEQRES 30 E 497 LYS ILE ARG PRO LEU TRP ARG HIS TYR TYR THR GLY THR SEQRES 31 E 497 GLN GLY LEU ILE PHE VAL VAL ASP CYS ALA ASP ARG ASP SEQRES 32 E 497 ARG ILE ASP GLU ALA ARG GLN GLU LEU HIS ARG ILE ILE SEQRES 33 E 497 ASN ASP ARG GLU MET ARG ASP ALA ILE ILE LEU ILE PHE SEQRES 34 E 497 ALA ASN LYS GLN ASP LEU PRO ASP ALA MET LYS PRO HIS SEQRES 35 E 497 GLU ILE GLN GLU LYS LEU GLY LEU THR ARG ILE ARG ASP SEQRES 36 E 497 ARG ASN TRP TYR VAL GLN PRO SER CYS ALA THR SER GLY SEQRES 37 E 497 ASP GLY LEU TYR GLU GLY LEU THR TRP LEU THR SER ASN SEQRES 38 E 497 TYR LYS SER LYS LEU ALA ALA ALA LEU GLU HIS HIS HIS SEQRES 39 E 497 HIS HIS HIS HET ZN E 735 1 HET MG E 736 1 HET GDP E 737 28 HET AF3 E 738 4 HET CA E 739 1 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM AF3 ALUMINUM FLUORIDE HETNAM CA CALCIUM ION FORMUL 2 ZN ZN 2+ FORMUL 3 MG MG 2+ FORMUL 4 GDP C10 H15 N5 O11 P2 FORMUL 5 AF3 AL F3 FORMUL 6 CA CA 2+ FORMUL 7 HOH *6(H2 O) HELIX 1 1 THR E 425 SER E 434 1 10 HELIX 2 2 CYS E 461 GLY E 472 1 12 HELIX 3 3 GLY E 487 GLU E 490 5 4 HELIX 4 4 LEU E 491 MET E 497 1 7 HELIX 5 5 GLY E 498 GLU E 507 1 10 HELIX 6 6 ASP E 523 VAL E 536 1 14 HELIX 7 7 GLU E 547 ARG E 558 1 12 HELIX 8 8 ASP E 559 ASN E 569 1 11 HELIX 9 9 VAL E 589 VAL E 596 1 8 HELIX 10 10 SER E 601 GLY E 612 1 12 HELIX 11 11 THR E 624 TYR E 632 1 9 HELIX 12 12 GLN E 634 GLY E 644 1 11 HELIX 13 13 THR E 657 LYS E 665 1 9 HELIX 14 14 GLU E 669 ALA E 677 1 9 HELIX 15 15 GLY E 25 GLY E 36 1 12 HELIX 16 16 GLN E 67 ARG E 71 5 5 HELIX 17 17 LEU E 73 TYR E 78 5 6 HELIX 18 18 ARG E 95 ASN E 108 1 14 HELIX 19 19 LYS E 131 LEU E 139 1 9 HELIX 20 20 GLY E 161 TYR E 173 1 13 SHEET 1 A 3 LEU E 459 THR E 460 0 SHEET 2 A 3 TRP E 451 SER E 453 -1 N TRP E 451 O THR E 460 SHEET 3 A 3 MET E 478 SER E 480 -1 O GLN E 479 N LEU E 452 SHEET 1 B 2 PRO E 576 LEU E 577 0 SHEET 2 B 2 GLU E 587 LEU E 588 -1 O GLU E 587 N LEU E 577 SHEET 1 C 6 PHE E 47 THR E 53 0 SHEET 2 C 6 LYS E 58 VAL E 64 -1 O ASP E 63 N ASN E 48 SHEET 3 C 6 GLU E 13 LEU E 19 1 N MET E 18 O TRP E 62 SHEET 4 C 6 GLY E 83 ASP E 89 1 O VAL E 87 N LEU E 19 SHEET 5 C 6 ILE E 116 ASN E 122 1 O LEU E 118 N LEU E 84 SHEET 6 C 6 ASN E 148 PRO E 153 1 O GLN E 152 N ILE E 119 LINK OG1 THR E 27 MG MG E 736 1555 1555 2.51 LINK OG1 THR E 44 MG MG E 736 1555 1555 2.17 LINK OD2 ASP E 68 CA CA E 739 1555 1555 2.51 LINK OD1 ASP E 68 CA CA E 739 1555 1555 3.02 LINK OE2 GLU E 98 CA CA E 739 1555 1555 2.98 LINK O HOH E 220 MG MG E 736 1555 1555 2.86 LINK O HOH E 232 CA CA E 739 1555 1555 2.80 LINK SG CYS E 441 ZN ZN E 735 1555 1555 2.41 LINK SG CYS E 444 ZN ZN E 735 1555 1555 2.06 LINK SG CYS E 461 ZN ZN E 735 1555 1555 2.29 LINK SG CYS E 464 ZN ZN E 735 1555 1555 2.27 LINK OE1 GLN E 479 CA CA E 739 1555 1555 2.95 LINK MG MG E 736 O2B GDP E 737 1555 1555 2.09 SITE 1 AC1 5 CYS E 441 CYS E 444 CYS E 461 CYS E 464 SITE 2 AC1 5 ARG E 527 SITE 1 AC2 7 LYS E 26 THR E 27 THR E 44 ASP E 63 SITE 2 AC2 7 HOH E 220 GDP E 737 AF3 E 738 SITE 1 AC3 20 ALA E 23 ALA E 24 GLY E 25 LYS E 26 SITE 2 AC3 20 THR E 27 THR E 28 THR E 41 ASN E 122 SITE 3 AC3 20 LYS E 123 ASP E 125 LEU E 126 CYS E 155 SITE 4 AC3 20 ALA E 156 THR E 157 HOH E 220 GLY E 466 SITE 5 AC3 20 ARG E 469 GLU E 470 MG E 736 AF3 E 738 SITE 1 AC4 13 ASP E 22 ALA E 23 LYS E 26 THR E 27 SITE 2 AC4 13 THR E 44 GLY E 65 GLY E 66 GLN E 67 SITE 3 AC4 13 HOH E 220 HOH E 230 ARG E 469 MG E 736 SITE 4 AC4 13 GDP E 737 SITE 1 AC5 4 ASP E 68 GLU E 98 HOH E 232 GLN E 479 CRYST1 146.450 146.450 49.620 90.00 90.00 120.00 P 62 6 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 0.006828 0.003942 0.000000 0.00000 SCALE2 0.000000 0.007885 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020153 0.00000