HEADER ENDOCYTOSIS 08-OCT-13 4N3Z TITLE CRYSTAL STRUCTURE OF RABEX-5DELTA AND RABAPTIN-5C21 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAB5 GDP/GTP EXCHANGE FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES, ISOFORM 2, 132-455; COMPND 5 SYNONYM: RABEX-5DELTA, RAP1, RABAPTIN-5-ASSOCIATED EXCHANGE FACTOR COMPND 6 FOR RAB5, RABEX-5; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RAB GTPASE-BINDING EFFECTOR PROTEIN 1; COMPND 11 CHAIN: B, C; COMPND 12 FRAGMENT: UNP RESIDUES 552-642; COMPND 13 SYNONYM: RABAPTIN-5C21, RABAPTIN-4, RABAPTIN-5, RABAPTIN-5ALPHA, COMPND 14 RENAL CARCINOMA ANTIGEN NY-REN-17; COMPND 15 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: RABEX5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETDUET1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: RABEP1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PETDUET1 KEYWDS RAB5, RABEX-5, RABAPTIN-5, GEF ACTIVITY, ENDOCYTOSIS, EARLY ENDOSOME EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZHANG,T.ZHANG,J.DING REVDAT 4 08-NOV-23 4N3Z 1 REMARK SEQADV REVDAT 3 15-NOV-17 4N3Z 1 REMARK REVDAT 2 09-DEC-15 4N3Z 1 JRNL REVDAT 1 23-JUL-14 4N3Z 0 JRNL AUTH Z.ZHANG,T.ZHANG,S.WANG,Z.GONG,C.TANG,J.CHEN,J.DING JRNL TITL MOLECULAR MECHANISM FOR RABEX-5 GEF ACTIVATION BY RABAPTIN-5 JRNL REF ELIFE V. 3 02687 2014 JRNL REFN ESSN 2050-084X JRNL PMID 24957337 JRNL DOI 10.7554/ELIFE.02687 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 3 NUMBER OF REFLECTIONS : 12008 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) : 0.267 REMARK 3 R VALUE (WORKING SET) : 0.264 REMARK 3 FREE R VALUE : 0.315 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 601 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 234 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 26.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE SET COUNT : 11 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3059 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.93000 REMARK 3 B22 (A**2) : -1.93000 REMARK 3 B33 (A**2) : 2.90000 REMARK 3 B12 (A**2) : -0.97000 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): 0.544 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.406 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 49.255 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.849 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.763 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3089 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4153 ; 1.268 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 394 ; 6.000 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;38.473 ;25.942 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 587 ;19.538 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;12.566 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 491 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2239 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3066 ; 2.835 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3050 ;53.470 ; 5.000 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 4N3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13730 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.64300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: 1TXU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M NAH2PO4/K2HPO4, 0.05% N-OCTYL REMARK 280 -BETA-D-GALACTOPYRANOSIDE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-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 56.29267 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 112.58533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 112.58533 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 56.29267 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 124 REMARK 465 GLY A 125 REMARK 465 HIS A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 465 SER A 132 REMARK 465 ILE A 133 REMARK 465 GLU A 134 REMARK 465 THR A 135 REMARK 465 ASP A 136 REMARK 465 ARG A 137 REMARK 465 VAL A 138 REMARK 465 SER A 139 REMARK 465 LYS A 140 REMARK 465 PHE A 149 REMARK 465 LYS A 161 REMARK 465 LEU A 162 REMARK 465 SER A 174 REMARK 465 ALA A 190 REMARK 465 GLU A 191 REMARK 465 ARG A 192 REMARK 465 MET A 193 REMARK 465 GLN A 194 REMARK 465 THR A 195 REMARK 465 ARG A 196 REMARK 465 GLY A 197 REMARK 465 LYS A 198 REMARK 465 VAL A 199 REMARK 465 PRO A 200 REMARK 465 PRO A 201 REMARK 465 GLU A 202 REMARK 465 ARG A 203 REMARK 465 VAL A 204 REMARK 465 TYR A 220 REMARK 465 LYS A 221 REMARK 465 TYR A 222 REMARK 465 VAL A 223 REMARK 465 PHE A 224 REMARK 465 CYS A 225 REMARK 465 PRO A 226 REMARK 465 GLU A 227 REMARK 465 THR A 228 REMARK 465 THR A 229 REMARK 465 ASP A 230 REMARK 465 LEU A 369 REMARK 465 ASP A 370 REMARK 465 ALA A 371 REMARK 465 GLN A 372 REMARK 465 SER A 373 REMARK 465 LEU A 374 REMARK 465 ASN A 375 REMARK 465 LEU A 376 REMARK 465 SER A 377 REMARK 465 GLN A 378 REMARK 465 GLU A 379 REMARK 465 ASP A 380 REMARK 465 PHE A 381 REMARK 465 ASP A 382 REMARK 465 ARG A 383 REMARK 465 TYR A 384 REMARK 465 MET A 385 REMARK 465 SER A 386 REMARK 465 GLN A 387 REMARK 465 MET A 388 REMARK 465 TYR A 389 REMARK 465 LYS A 390 REMARK 465 VAL A 431 REMARK 465 GLU A 432 REMARK 465 LYS A 433 REMARK 465 MET B 551 REMARK 465 GLU B 552 REMARK 465 ARG B 635 REMARK 465 GLU B 636 REMARK 465 GLN B 637 REMARK 465 VAL B 638 REMARK 465 SER B 639 REMARK 465 GLU B 640 REMARK 465 GLU B 641 REMARK 465 LEU B 642 REMARK 465 MET C 551 REMARK 465 GLU C 552 REMARK 465 GLU C 636 REMARK 465 GLN C 637 REMARK 465 VAL C 638 REMARK 465 SER C 639 REMARK 465 GLU C 640 REMARK 465 GLU C 641 REMARK 465 LEU C 642 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 GLU A 141 CG CD OE1 OE2 REMARK 470 PHE A 142 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE A 143 CG1 CG2 CD1 REMARK 470 GLU A 144 CG CD OE1 OE2 REMARK 470 PHE A 145 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 146 CG CD1 CD2 REMARK 470 LYS A 147 CG CD CE NZ REMARK 470 THR A 148 OG1 CG2 REMARK 470 HIS A 150 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 151 CG CD CE NZ REMARK 470 THR A 152 OG1 CG2 REMARK 470 GLN A 154 CG CD OE1 NE2 REMARK 470 GLU A 155 CG CD OE1 OE2 REMARK 470 ILE A 156 CG1 CG2 CD1 REMARK 470 TYR A 157 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 GLN A 159 CG CD OE1 NE2 REMARK 470 THR A 160 OG1 CG2 REMARK 470 PHE A 163 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 164 CG CD1 CD2 REMARK 470 GLU A 165 CG CD OE1 OE2 REMARK 470 MET A 167 CG SD CE REMARK 470 HIS A 168 CG ND1 CD2 CE1 NE2 REMARK 470 TYR A 169 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 170 CG CD CE NZ REMARK 470 ARG A 171 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 172 CG OD1 OD2 REMARK 470 LEU A 173 CG CD1 CD2 REMARK 470 ILE A 175 CG1 CG2 CD1 REMARK 470 GLU A 176 CG CD OE1 OE2 REMARK 470 GLU A 177 CG CD OE1 OE2 REMARK 470 GLN A 178 CG CD OE1 NE2 REMARK 470 SER A 179 OG REMARK 470 GLU A 180 CG CD OE1 OE2 REMARK 470 GLN A 183 CG CD OE1 NE2 REMARK 470 ASP A 184 CG OD1 OD2 REMARK 470 PHE A 185 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 186 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 HIS A 187 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 188 CG OD1 ND2 REMARK 470 VAL A 189 CG1 CG2 REMARK 470 GLU A 205 CG CD OE1 OE2 REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 ILE A 207 CG1 CG2 CD1 REMARK 470 MET A 208 CG SD CE REMARK 470 ASP A 209 CG OD1 OD2 REMARK 470 GLN A 210 CG CD OE1 NE2 REMARK 470 ILE A 211 CG1 CG2 CD1 REMARK 470 GLU A 212 CG CD OE1 OE2 REMARK 470 LYS A 213 CG CD CE NZ REMARK 470 TYR A 214 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE A 215 CG1 CG2 CD1 REMARK 470 MET A 216 CG SD CE REMARK 470 THR A 217 OG1 CG2 REMARK 470 ARG A 218 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 219 CG CD1 CD2 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 GLU A 232 64.16 61.51 REMARK 500 ALA A 244 -71.01 -57.69 REMARK 500 LEU A 245 6.09 -59.57 REMARK 500 MET A 252 -7.26 87.11 REMARK 500 ARG A 282 -73.76 -87.44 REMARK 500 GLU A 308 139.18 -175.77 REMARK 500 ARG A 330 70.82 52.45 REMARK 500 CYS A 342 154.14 177.34 REMARK 500 PRO A 344 -8.55 -51.16 REMARK 500 ARG A 346 -71.08 -54.00 REMARK 500 MET A 348 -170.36 -68.10 REMARK 500 GLN B 587 159.11 168.00 REMARK 500 SER B 588 64.72 37.33 REMARK 500 MET B 632 -74.10 -72.38 REMARK 500 SER C 589 -70.82 -59.77 REMARK 500 HIS C 594 70.77 37.77 REMARK 500 GLN C 595 -74.81 -100.03 REMARK 500 ILE C 596 72.27 51.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 C 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4N3X RELATED DB: PDB REMARK 900 RELATED ID: 4N3Y RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE REFERENCE SEQUENCE OF CHAIN A IS ISOFORM 2 OF Q9UJ41, AND REMARK 999 RESIDUES 387-408 HAVE BEEN DELETED. DBREF 4N3Z A 132 433 UNP Q9UJ41 RABX5_HUMAN 132 455 DBREF 4N3Z B 552 642 UNP Q15276 RABE1_HUMAN 552 642 DBREF 4N3Z C 552 642 UNP Q15276 RABE1_HUMAN 552 642 SEQADV 4N3Z MET A 124 UNP Q9UJ41 EXPRESSION TAG SEQADV 4N3Z GLY A 125 UNP Q9UJ41 EXPRESSION TAG SEQADV 4N3Z HIS A 126 UNP Q9UJ41 EXPRESSION TAG SEQADV 4N3Z HIS A 127 UNP Q9UJ41 EXPRESSION TAG SEQADV 4N3Z HIS A 128 UNP Q9UJ41 EXPRESSION TAG SEQADV 4N3Z HIS A 129 UNP Q9UJ41 EXPRESSION TAG SEQADV 4N3Z HIS A 130 UNP Q9UJ41 EXPRESSION TAG SEQADV 4N3Z HIS A 131 UNP Q9UJ41 EXPRESSION TAG SEQADV 4N3Z A UNP Q9UJ41 GLY 387 DELETION SEQADV 4N3Z A UNP Q9UJ41 GLN 388 DELETION SEQADV 4N3Z A UNP Q9UJ41 THR 389 DELETION SEQADV 4N3Z A UNP Q9UJ41 SER 390 DELETION SEQADV 4N3Z A UNP Q9UJ41 PRO 391 DELETION SEQADV 4N3Z A UNP Q9UJ41 ARG 392 DELETION SEQADV 4N3Z A UNP Q9UJ41 LYS 393 DELETION SEQADV 4N3Z A UNP Q9UJ41 GLN 394 DELETION SEQADV 4N3Z A UNP Q9UJ41 GLU 395 DELETION SEQADV 4N3Z A UNP Q9UJ41 ALA 396 DELETION SEQADV 4N3Z A UNP Q9UJ41 GLU 397 DELETION SEQADV 4N3Z A UNP Q9UJ41 SER 398 DELETION SEQADV 4N3Z A UNP Q9UJ41 TRP 399 DELETION SEQADV 4N3Z A UNP Q9UJ41 SER 400 DELETION SEQADV 4N3Z A UNP Q9UJ41 PRO 401 DELETION SEQADV 4N3Z A UNP Q9UJ41 ASP 402 DELETION SEQADV 4N3Z A UNP Q9UJ41 ALA 403 DELETION SEQADV 4N3Z A UNP Q9UJ41 CYS 404 DELETION SEQADV 4N3Z A UNP Q9UJ41 LEU 405 DELETION SEQADV 4N3Z A UNP Q9UJ41 GLY 406 DELETION SEQADV 4N3Z A UNP Q9UJ41 VAL 407 DELETION SEQADV 4N3Z A UNP Q9UJ41 LYS 408 DELETION SEQADV 4N3Z MET B 551 UNP Q15276 EXPRESSION TAG SEQADV 4N3Z MET C 551 UNP Q15276 EXPRESSION TAG SEQRES 1 A 310 MET GLY HIS HIS HIS HIS HIS HIS SER ILE GLU THR ASP SEQRES 2 A 310 ARG VAL SER LYS GLU PHE ILE GLU PHE LEU LYS THR PHE SEQRES 3 A 310 HIS LYS THR GLY GLN GLU ILE TYR LYS GLN THR LYS LEU SEQRES 4 A 310 PHE LEU GLU GLY MET HIS TYR LYS ARG ASP LEU SER ILE SEQRES 5 A 310 GLU GLU GLN SER GLU CYS ALA GLN ASP PHE TYR HIS ASN SEQRES 6 A 310 VAL ALA GLU ARG MET GLN THR ARG GLY LYS VAL PRO PRO SEQRES 7 A 310 GLU ARG VAL GLU LYS ILE MET ASP GLN ILE GLU LYS TYR SEQRES 8 A 310 ILE MET THR ARG LEU TYR LYS TYR VAL PHE CYS PRO GLU SEQRES 9 A 310 THR THR ASP ASP GLU LYS LYS ASP LEU ALA ILE GLN LYS SEQRES 10 A 310 ARG ILE ARG ALA LEU ARG TRP VAL THR PRO GLN MET LEU SEQRES 11 A 310 CYS VAL PRO VAL ASN GLU ASP ILE PRO GLU VAL SER ASP SEQRES 12 A 310 MET VAL VAL LYS ALA ILE THR ASP ILE ILE GLU MET ASP SEQRES 13 A 310 SER LYS ARG VAL PRO ARG ASP LYS LEU ALA CYS ILE THR SEQRES 14 A 310 LYS CYS SER LYS HIS ILE PHE ASN ALA ILE LYS ILE THR SEQRES 15 A 310 LYS ASN GLU PRO ALA SER ALA ASP ASP PHE LEU PRO THR SEQRES 16 A 310 LEU ILE TYR ILE VAL LEU LYS GLY ASN PRO PRO ARG LEU SEQRES 17 A 310 GLN SER ASN ILE GLN TYR ILE THR ARG PHE CYS ASN PRO SEQRES 18 A 310 SER ARG LEU MET THR GLY GLU ASP GLY TYR TYR PHE THR SEQRES 19 A 310 ASN LEU CYS CYS ALA VAL ALA PHE ILE GLU LYS LEU ASP SEQRES 20 A 310 ALA GLN SER LEU ASN LEU SER GLN GLU ASP PHE ASP ARG SEQRES 21 A 310 TYR MET SER GLN MET TYR LYS ASN LEU ASP LEU LEU SER SEQRES 22 A 310 GLN LEU ASN GLU ARG GLN GLU ARG ILE MET ASN GLU ALA SEQRES 23 A 310 LYS LYS LEU GLU LYS ASP LEU ILE ASP TRP THR ASP GLY SEQRES 24 A 310 ILE ALA ARG GLU VAL GLN ASP ILE VAL GLU LYS SEQRES 1 B 92 MET GLU THR ARG ASP GLN VAL LYS LYS LEU GLN LEU MET SEQRES 2 B 92 LEU ARG GLN ALA ASN ASP GLN LEU GLU LYS THR MET LYS SEQRES 3 B 92 ASP LYS GLN GLU LEU GLU ASP PHE ILE LYS GLN SER SER SEQRES 4 B 92 GLU ASP SER SER HIS GLN ILE SER ALA LEU VAL LEU ARG SEQRES 5 B 92 ALA GLN ALA SER GLU ILE LEU LEU GLU GLU LEU GLN GLN SEQRES 6 B 92 GLY LEU SER GLN ALA LYS ARG ASP VAL GLN GLU GLN MET SEQRES 7 B 92 ALA VAL LEU MET GLN SER ARG GLU GLN VAL SER GLU GLU SEQRES 8 B 92 LEU SEQRES 1 C 92 MET GLU THR ARG ASP GLN VAL LYS LYS LEU GLN LEU MET SEQRES 2 C 92 LEU ARG GLN ALA ASN ASP GLN LEU GLU LYS THR MET LYS SEQRES 3 C 92 ASP LYS GLN GLU LEU GLU ASP PHE ILE LYS GLN SER SER SEQRES 4 C 92 GLU ASP SER SER HIS GLN ILE SER ALA LEU VAL LEU ARG SEQRES 5 C 92 ALA GLN ALA SER GLU ILE LEU LEU GLU GLU LEU GLN GLN SEQRES 6 C 92 GLY LEU SER GLN ALA LYS ARG ASP VAL GLN GLU GLN MET SEQRES 7 C 92 ALA VAL LEU MET GLN SER ARG GLU GLN VAL SER GLU GLU SEQRES 8 C 92 LEU HET PO4 A 501 5 HET PO4 B 701 5 HET PO4 C 701 5 HETNAM PO4 PHOSPHATE ION FORMUL 4 PO4 3(O4 P 3-) HELIX 1 1 GLU A 141 THR A 148 1 8 HELIX 2 2 LYS A 151 THR A 160 1 10 HELIX 3 3 LEU A 164 ARG A 171 1 8 HELIX 4 4 GLU A 176 VAL A 189 1 14 HELIX 5 5 LYS A 206 LEU A 219 1 14 HELIX 6 6 ASP A 235 LEU A 245 1 11 HELIX 7 7 ARG A 246 VAL A 248 5 3 HELIX 8 8 ILE A 261 MET A 278 1 18 HELIX 9 9 VAL A 283 ASN A 307 1 25 HELIX 10 10 SER A 311 LYS A 325 1 15 HELIX 11 11 ARG A 330 PHE A 341 1 12 HELIX 12 12 GLU A 351 GLU A 367 1 17 HELIX 13 13 LEU A 392 GLN A 428 1 37 HELIX 14 14 ARG B 554 LYS B 586 1 33 HELIX 15 15 ILE B 596 SER B 634 1 39 HELIX 16 16 ARG C 554 GLU C 590 1 37 HELIX 17 17 ILE C 596 SER C 634 1 39 SITE 1 AC1 2 LYS A 270 HIS A 297 SITE 1 AC2 2 ASP B 591 HIS C 594 SITE 1 AC3 5 GLN B 627 GLN C 625 MET C 628 ALA C 629 SITE 2 AC3 5 MET C 632 CRYST1 87.140 87.140 168.878 90.00 90.00 120.00 P 31 2 1 12 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 0.011476 0.006626 0.000000 0.00000 SCALE2 0.000000 0.013251 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005921 0.00000