HEADER PROTEIN TRANSPORT 06-JUN-20 6ZAY TITLE CRYSTAL STRUCTURE OF ATG16L IN COMPLEX WITH GDP-BOUND RAB33B COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-33B; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: AUTOPHAGY-RELATED PROTEIN 16-1; COMPND 7 CHAIN: C, D; COMPND 8 SYNONYM: APG16-LIKE 1; COMPND 9 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: RAB33B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASTMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: POPIN; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_COMMON: MOUSE; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 GENE: ATG16L1, APG16L; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASTMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PRSF KEYWDS ATG16L; AUTOPHAGY; AUTOPHAGOSOME FORMATION; RAB33B, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.PANTOOM,Y.W.WU REVDAT 3 24-JAN-24 6ZAY 1 REMARK REVDAT 2 13-OCT-21 6ZAY 1 JRNL REVDAT 1 30-SEP-20 6ZAY 0 JRNL AUTH S.PANTOOM,G.KONSTANTINIDIS,S.VOSS,H.HAN,O.HOFNAGEL,Z.LI, JRNL AUTH 2 Y.W.WU JRNL TITL RAB33B RECRUITS THE ATG16L1 COMPLEX TO THE PHAGOPHORE VIA A JRNL TITL 2 NONCANONICAL RAB BINDING PROTEIN. JRNL REF AUTOPHAGY V. 17 2290 2021 JRNL REFN ESSN 1554-8635 JRNL PMID 32960676 JRNL DOI 10.1080/15548627.2020.1822629 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 1.9_1692 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 46278 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2317 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4252 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 141 REMARK 3 SOLVENT ATOMS : 179 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.270 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ZAY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109205. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97714 REMARK 200 MONOCHROMATOR : SI(III) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46452 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 49.572 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.11690 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 13.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1Z06 AND 3Q8T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG3350, 0.2M POTASSIUM REMARK 280 THIOCYANATE AND 0.1M SODIUM POTASSIUM PHOSPHATE, PH 6.2, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 28.50500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.18500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 66.05500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 77.18500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.50500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 66.05500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 27 REMARK 465 PRO A 28 REMARK 465 MET A 29 REMARK 465 LEU A 205 REMARK 465 MET A 206 REMARK 465 LEU A 207 REMARK 465 SER A 208 REMARK 465 GLN A 209 REMARK 465 PRO A 210 REMARK 465 PRO A 211 REMARK 465 ASP A 212 REMARK 465 ASN A 213 REMARK 465 GLY A 214 REMARK 465 ILE A 215 REMARK 465 ILE A 216 REMARK 465 LEU A 217 REMARK 465 LYS A 218 REMARK 465 GLU C 226 REMARK 465 ALA C 227 REMARK 465 ALA C 228 REMARK 465 LYS C 229 REMARK 465 GLU C 230 REMARK 465 PRO C 231 REMARK 465 LEU C 232 REMARK 465 PRO C 233 REMARK 465 VAL C 234 REMARK 465 GLU C 235 REMARK 465 GLN C 236 REMARK 465 ASP C 237 REMARK 465 ASP C 238 REMARK 465 ASP C 239 REMARK 465 ILE C 240 REMARK 465 GLU C 241 REMARK 465 VAL C 242 REMARK 465 ILE C 243 REMARK 465 VAL C 244 REMARK 465 ASP C 245 REMARK 465 GLU C 246 REMARK 465 THR C 247 REMARK 465 SER C 248 REMARK 465 ASP C 249 REMARK 465 HIS C 250 REMARK 465 THR C 251 REMARK 465 GLU C 252 REMARK 465 GLU C 253 REMARK 465 THR C 254 REMARK 465 SER C 255 REMARK 465 PRO C 256 REMARK 465 VAL C 257 REMARK 465 ARG C 258 REMARK 465 ALA C 259 REMARK 465 VAL C 260 REMARK 465 SER C 261 REMARK 465 ARG C 262 REMARK 465 ALA C 263 REMARK 465 ALA C 264 REMARK 465 THR C 265 REMARK 465 GLY B 27 REMARK 465 PRO B 28 REMARK 465 MET B 29 REMARK 465 LEU B 205 REMARK 465 MET B 206 REMARK 465 LEU B 207 REMARK 465 SER B 208 REMARK 465 GLN B 209 REMARK 465 PRO B 210 REMARK 465 PRO B 211 REMARK 465 ASP B 212 REMARK 465 ASN B 213 REMARK 465 GLY B 214 REMARK 465 ILE B 215 REMARK 465 ILE B 216 REMARK 465 LEU B 217 REMARK 465 LYS B 218 REMARK 465 GLU D 226 REMARK 465 ALA D 227 REMARK 465 ALA D 228 REMARK 465 LYS D 229 REMARK 465 GLU D 230 REMARK 465 PRO D 231 REMARK 465 LEU D 232 REMARK 465 PRO D 233 REMARK 465 VAL D 234 REMARK 465 GLU D 235 REMARK 465 GLN D 236 REMARK 465 ASP D 237 REMARK 465 ASP D 238 REMARK 465 ASP D 239 REMARK 465 ILE D 240 REMARK 465 GLU D 241 REMARK 465 VAL D 242 REMARK 465 ILE D 243 REMARK 465 VAL D 244 REMARK 465 ASP D 245 REMARK 465 GLU D 246 REMARK 465 THR D 247 REMARK 465 SER D 248 REMARK 465 ASP D 249 REMARK 465 HIS D 250 REMARK 465 THR D 251 REMARK 465 GLU D 252 REMARK 465 GLU D 253 REMARK 465 THR D 254 REMARK 465 SER D 255 REMARK 465 PRO D 256 REMARK 465 VAL D 257 REMARK 465 ARG D 258 REMARK 465 ALA D 259 REMARK 465 VAL D 260 REMARK 465 SER D 261 REMARK 465 ARG D 262 REMARK 465 ALA D 263 REMARK 465 ALA D 264 REMARK 465 THR D 265 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 VAL A 68 147.53 -175.28 REMARK 500 LYS A 149 35.79 73.42 REMARK 500 LEU A 152 58.59 -95.61 REMARK 500 ASN A 185 -114.65 38.57 REMARK 500 LYS B 97 -61.88 -28.66 REMARK 500 ASN B 185 -117.97 46.07 REMARK 500 ASP D 147 -0.76 -59.15 REMARK 500 GLU D 156 -61.38 -96.55 REMARK 500 THR D 161 -89.28 -136.00 REMARK 500 LEU D 162 -95.68 -11.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH D 315 DISTANCE = 7.70 ANGSTROMS 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 A 306 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 47 OG1 REMARK 620 2 THR A 65 OG1 64.9 REMARK 620 3 GDP A 307 O1B 71.1 108.9 REMARK 620 4 HOH A 402 O 60.4 53.6 56.7 REMARK 620 5 HOH A 413 O 123.7 77.3 84.8 63.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 310 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 47 OG1 REMARK 620 2 GLU B 63 O 114.8 REMARK 620 3 THR B 65 OG1 58.6 89.5 REMARK 620 4 GDP B 311 O1B 58.2 172.0 89.4 REMARK 620 5 GDP B 311 O2A 99.1 108.2 156.4 70.8 REMARK 620 6 HOH B 404 O 111.0 105.3 68.6 81.7 118.9 REMARK 620 N 1 2 3 4 5 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP B 311 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6Y09 RELATED DB: PDB DBREF 6ZAY A 30 218 UNP Q9H082 RB33B_HUMAN 30 218 DBREF 6ZAY C 141 265 UNP Q8C0J2 A16L1_MOUSE 141 265 DBREF 6ZAY B 30 218 UNP Q9H082 RB33B_HUMAN 30 218 DBREF 6ZAY D 141 265 UNP Q8C0J2 A16L1_MOUSE 141 265 SEQADV 6ZAY GLY A 27 UNP Q9H082 EXPRESSION TAG SEQADV 6ZAY PRO A 28 UNP Q9H082 EXPRESSION TAG SEQADV 6ZAY MET A 29 UNP Q9H082 EXPRESSION TAG SEQADV 6ZAY MET C 140 UNP Q8C0J2 INITIATING METHIONINE SEQADV 6ZAY GLY B 27 UNP Q9H082 EXPRESSION TAG SEQADV 6ZAY PRO B 28 UNP Q9H082 EXPRESSION TAG SEQADV 6ZAY MET B 29 UNP Q9H082 EXPRESSION TAG SEQADV 6ZAY MET D 140 UNP Q8C0J2 INITIATING METHIONINE SEQRES 1 A 192 GLY PRO MET ARG SER ARG ILE PHE LYS ILE ILE VAL ILE SEQRES 2 A 192 GLY ASP SER ASN VAL GLY LYS THR CYS LEU THR TYR ARG SEQRES 3 A 192 PHE CYS ALA GLY ARG PHE PRO ASP ARG THR GLU ALA THR SEQRES 4 A 192 ILE GLY VAL ASP PHE ARG GLU ARG ALA VAL GLU ILE ASP SEQRES 5 A 192 GLY GLU ARG ILE LYS ILE GLN LEU TRP ASP THR ALA GLY SEQRES 6 A 192 GLN GLU ARG PHE ARG LYS SER MET VAL GLN HIS TYR TYR SEQRES 7 A 192 ARG ASN VAL HIS ALA VAL VAL PHE VAL TYR ASP MET THR SEQRES 8 A 192 ASN MET ALA SER PHE HIS SER LEU PRO SER TRP ILE GLU SEQRES 9 A 192 GLU CYS LYS GLN HIS LEU LEU ALA ASN ASP ILE PRO ARG SEQRES 10 A 192 ILE LEU VAL GLY ASN LYS CYS ASP LEU ARG SER ALA ILE SEQRES 11 A 192 GLN VAL PRO THR ASP LEU ALA GLN LYS PHE ALA ASP THR SEQRES 12 A 192 HIS SER MET PRO LEU PHE GLU THR SER ALA LYS ASN PRO SEQRES 13 A 192 ASN ASP ASN ASP HIS VAL GLU ALA ILE PHE MET THR LEU SEQRES 14 A 192 ALA HIS LYS LEU LYS SER HIS LYS PRO LEU MET LEU SER SEQRES 15 A 192 GLN PRO PRO ASP ASN GLY ILE ILE LEU LYS SEQRES 1 C 126 MET LEU GLU THR ASN CYS LEU ASP LEU ARG THR LYS LEU SEQRES 2 C 126 GLN ASP LEU GLU VAL ALA ASN GLN THR LEU LYS ASP GLU SEQRES 3 C 126 TYR ASP ALA LEU GLN ILE THR PHE THR ALA LEU GLU GLU SEQRES 4 C 126 LYS LEU ARG LYS THR THR GLU GLU ASN GLN GLU LEU VAL SEQRES 5 C 126 THR ARG TRP MET ALA GLU LYS ALA GLN GLU ALA ASN ARG SEQRES 6 C 126 LEU ASN ALA GLU ASN GLU LYS ASP SER ARG ARG ARG GLN SEQRES 7 C 126 ALA ARG LEU GLN LYS GLU LEU ALA GLU ALA ALA LYS GLU SEQRES 8 C 126 PRO LEU PRO VAL GLU GLN ASP ASP ASP ILE GLU VAL ILE SEQRES 9 C 126 VAL ASP GLU THR SER ASP HIS THR GLU GLU THR SER PRO SEQRES 10 C 126 VAL ARG ALA VAL SER ARG ALA ALA THR SEQRES 1 B 192 GLY PRO MET ARG SER ARG ILE PHE LYS ILE ILE VAL ILE SEQRES 2 B 192 GLY ASP SER ASN VAL GLY LYS THR CYS LEU THR TYR ARG SEQRES 3 B 192 PHE CYS ALA GLY ARG PHE PRO ASP ARG THR GLU ALA THR SEQRES 4 B 192 ILE GLY VAL ASP PHE ARG GLU ARG ALA VAL GLU ILE ASP SEQRES 5 B 192 GLY GLU ARG ILE LYS ILE GLN LEU TRP ASP THR ALA GLY SEQRES 6 B 192 GLN GLU ARG PHE ARG LYS SER MET VAL GLN HIS TYR TYR SEQRES 7 B 192 ARG ASN VAL HIS ALA VAL VAL PHE VAL TYR ASP MET THR SEQRES 8 B 192 ASN MET ALA SER PHE HIS SER LEU PRO SER TRP ILE GLU SEQRES 9 B 192 GLU CYS LYS GLN HIS LEU LEU ALA ASN ASP ILE PRO ARG SEQRES 10 B 192 ILE LEU VAL GLY ASN LYS CYS ASP LEU ARG SER ALA ILE SEQRES 11 B 192 GLN VAL PRO THR ASP LEU ALA GLN LYS PHE ALA ASP THR SEQRES 12 B 192 HIS SER MET PRO LEU PHE GLU THR SER ALA LYS ASN PRO SEQRES 13 B 192 ASN ASP ASN ASP HIS VAL GLU ALA ILE PHE MET THR LEU SEQRES 14 B 192 ALA HIS LYS LEU LYS SER HIS LYS PRO LEU MET LEU SER SEQRES 15 B 192 GLN PRO PRO ASP ASN GLY ILE ILE LEU LYS SEQRES 1 D 126 MET LEU GLU THR ASN CYS LEU ASP LEU ARG THR LYS LEU SEQRES 2 D 126 GLN ASP LEU GLU VAL ALA ASN GLN THR LEU LYS ASP GLU SEQRES 3 D 126 TYR ASP ALA LEU GLN ILE THR PHE THR ALA LEU GLU GLU SEQRES 4 D 126 LYS LEU ARG LYS THR THR GLU GLU ASN GLN GLU LEU VAL SEQRES 5 D 126 THR ARG TRP MET ALA GLU LYS ALA GLN GLU ALA ASN ARG SEQRES 6 D 126 LEU ASN ALA GLU ASN GLU LYS ASP SER ARG ARG ARG GLN SEQRES 7 D 126 ALA ARG LEU GLN LYS GLU LEU ALA GLU ALA ALA LYS GLU SEQRES 8 D 126 PRO LEU PRO VAL GLU GLN ASP ASP ASP ILE GLU VAL ILE SEQRES 9 D 126 VAL ASP GLU THR SER ASP HIS THR GLU GLU THR SER PRO SEQRES 10 D 126 VAL ARG ALA VAL SER ARG ALA ALA THR HET PO4 A 301 5 HET PO4 A 302 5 HET PEG A 303 7 HET PEG A 304 7 HET EDO A 305 4 HET MG A 306 1 HET GDP A 307 28 HET PO4 C 301 5 HET PO4 B 301 5 HET PO4 B 302 5 HET EDO B 303 4 HET EDO B 304 4 HET PEG B 305 7 HET EDO B 306 4 HET PEG B 307 7 HET PEG B 308 7 HET PEG B 309 7 HET MG B 310 1 HET GDP B 311 28 HETNAM PO4 PHOSPHATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 5 PO4 5(O4 P 3-) FORMUL 7 PEG 6(C4 H10 O3) FORMUL 9 EDO 4(C2 H6 O2) FORMUL 10 MG 2(MG 2+) FORMUL 11 GDP 2(C10 H15 N5 O11 P2) FORMUL 24 HOH *179(H2 O) HELIX 1 AA1 GLY A 45 GLY A 56 1 12 HELIX 2 AA2 GLN A 92 LYS A 97 1 6 HELIX 3 AA3 MET A 99 ARG A 105 1 7 HELIX 4 AA4 ASN A 118 SER A 124 1 7 HELIX 5 AA5 SER A 124 LEU A 136 1 13 HELIX 6 AA6 LEU A 152 ILE A 156 5 5 HELIX 7 AA7 PRO A 159 HIS A 170 1 12 HELIX 8 AA8 HIS A 187 HIS A 202 1 16 HELIX 9 AA9 ASN C 144 ILE C 171 1 28 HELIX 10 AB1 ILE C 171 LEU C 220 1 50 HELIX 11 AB2 GLY B 45 GLY B 56 1 12 HELIX 12 AB3 GLN B 92 ARG B 96 5 5 HELIX 13 AB4 MET B 99 ARG B 105 1 7 HELIX 14 AB5 ASN B 118 SER B 124 1 7 HELIX 15 AB6 SER B 124 LEU B 136 1 13 HELIX 16 AB7 LEU B 152 ILE B 156 5 5 HELIX 17 AB8 PRO B 159 HIS B 170 1 12 HELIX 18 AB9 HIS B 187 HIS B 202 1 16 HELIX 19 AC1 CYS D 145 ARG D 149 5 5 HELIX 20 AC2 THR D 150 ALA D 158 1 9 HELIX 21 AC3 THR D 161 GLU D 223 1 63 SHEET 1 AA1 6 VAL A 68 ILE A 77 0 SHEET 2 AA1 6 GLU A 80 THR A 89 -1 O ILE A 82 N VAL A 75 SHEET 3 AA1 6 ARG A 32 ILE A 39 1 N ARG A 32 O LYS A 83 SHEET 4 AA1 6 ALA A 109 ASP A 115 1 O VAL A 111 N ILE A 37 SHEET 5 AA1 6 ARG A 143 ASN A 148 1 O ILE A 144 N PHE A 112 SHEET 6 AA1 6 LEU A 174 GLU A 176 1 O PHE A 175 N GLY A 147 SHEET 1 AA2 6 VAL B 68 ILE B 77 0 SHEET 2 AA2 6 GLU B 80 THR B 89 -1 O ASP B 88 N ASP B 69 SHEET 3 AA2 6 ARG B 32 ILE B 39 1 N VAL B 38 O TRP B 87 SHEET 4 AA2 6 ALA B 109 ASP B 115 1 O VAL B 111 N ILE B 37 SHEET 5 AA2 6 ARG B 143 ASN B 148 1 O ILE B 144 N PHE B 112 SHEET 6 AA2 6 LEU B 174 GLU B 176 1 O PHE B 175 N GLY B 147 LINK OG1 THR A 47 MG MG A 306 1555 1555 2.68 LINK OG1 THR A 65 MG MG A 306 1555 1555 2.69 LINK MG MG A 306 O1B GDP A 307 1555 1555 2.57 LINK MG MG A 306 O HOH A 402 1555 1555 2.69 LINK MG MG A 306 O HOH A 413 1555 1555 2.70 LINK OG1 THR B 47 MG MG B 310 1555 1555 2.91 LINK O GLU B 63 MG MG B 310 1555 1555 2.84 LINK OG1 THR B 65 MG MG B 310 1555 1555 2.86 LINK MG MG B 310 O1B GDP B 311 1555 1555 2.97 LINK MG MG B 310 O2A GDP B 311 1555 1555 2.89 LINK MG MG B 310 O HOH B 404 1555 1555 2.82 SITE 1 AC1 6 LYS A 133 ALA A 138 THR B 160 GLU B 176 SITE 2 AC1 6 ASN B 185 PEG B 307 SITE 1 AC2 7 GLN A 164 LEU A 174 GLU A 176 ASP A 186 SITE 2 AC2 7 LYS B 133 PO4 B 301 HOH B 410 SITE 1 AC3 7 ASN A 43 ASP A 115 THR A 117 LYS A 149 SITE 2 AC3 7 LEU A 152 GDP A 307 HOH A 408 SITE 1 AC4 5 HIS A 123 LEU A 162 PHE A 166 HOH A 430 SITE 2 AC4 5 HOH A 446 SITE 1 AC5 7 ILE A 129 CYS A 132 LYS A 133 LEU A 136 SITE 2 AC5 7 ARG A 143 ASN B 185 HOH B 415 SITE 1 AC6 6 THR A 47 GLU A 63 THR A 65 GDP A 307 SITE 2 AC6 6 HOH A 402 HOH A 413 SITE 1 AC7 19 ASN A 43 VAL A 44 GLY A 45 LYS A 46 SITE 2 AC7 19 THR A 47 CYS A 48 PHE A 58 THR A 62 SITE 3 AC7 19 ASN A 148 LYS A 149 ASP A 151 LEU A 152 SITE 4 AC7 19 SER A 178 ALA A 179 LYS A 180 PEG A 303 SITE 5 AC7 19 MG A 306 HOH A 402 HOH A 413 SITE 1 AC8 3 GLU C 197 TRP D 194 GLU D 197 SITE 1 AC9 7 THR A 160 GLU A 176 ASN A 185 PO4 A 302 SITE 2 AC9 7 LYS B 133 LEU B 136 ALA B 138 SITE 1 AD1 4 ARG B 94 GLU C 186 GLN D 188 VAL D 191 SITE 1 AD2 6 ASN A 185 ILE B 129 CYS B 132 LEU B 136 SITE 2 AD2 6 ARG B 143 HOH B 413 SITE 1 AD3 3 ARG B 52 GLY B 56 HOH B 421 SITE 1 AD4 3 ALA B 120 HIS B 123 SER B 124 SITE 1 AD5 3 HIS A 187 PRO B 126 HIS B 170 SITE 1 AD6 7 LYS A 133 GLN A 134 PO4 A 301 LEU B 174 SITE 2 AD6 7 GLU B 176 ASP B 186 HOH B 447 SITE 1 AD7 8 TYR B 104 ASN B 106 VAL B 107 LEU B 136 SITE 2 AD7 8 LEU B 137 ILE B 141 HOH B 429 HOH B 470 SITE 1 AD8 3 SER B 127 TRP B 128 GLU B 131 SITE 1 AD9 5 THR B 47 GLU B 63 THR B 65 GDP B 311 SITE 2 AD9 5 HOH B 404 SITE 1 AE1 18 ASN B 43 VAL B 44 GLY B 45 LYS B 46 SITE 2 AE1 18 THR B 47 CYS B 48 PHE B 58 THR B 62 SITE 3 AE1 18 ASN B 148 LYS B 149 ASP B 151 LEU B 152 SITE 4 AE1 18 SER B 178 ALA B 179 LYS B 180 MG B 310 SITE 5 AE1 18 HOH B 404 HOH B 434 CRYST1 57.010 132.110 154.370 90.00 90.00 90.00 P 21 21 21 8 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 0.017541 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007569 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006478 0.00000