PDB Short entry for 3Q5D HEADER HYDROLASE 28-DEC-10 3Q5D TITLE CRYSTAL STRUCTURE OF HUMAN ATLASTIN-1 (RESIDUES 1-447) BOUND TO GDP, TITLE 2 CRYSTAL FORM 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATLASTIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: G AND MIDDLE DOMAIN, UNP RESIDUES 1-447; COMPND 5 SYNONYM: BRAIN-SPECIFIC GTP-BINDING PROTEIN, GTP-BINDING PROTEIN 3, COMPND 6 GBP-3, HGBP3, GUANINE NUCLEOTIDE-BINDING PROTEIN 3, SPASTIC COMPND 7 PARAPLEGIA 3 PROTEIN A; COMPND 8 EC: 3.6.5.-; 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: ATL1, ATLASTIN-1 (RESIDUES 1-447), GBP3, SPG3A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS G PROTEIN, GTPASE, GDP/GTP BINDING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.J.BYRNES,H.SONDERMANN REVDAT 3 08-NOV-17 3Q5D 1 REMARK REVDAT 2 20-APR-11 3Q5D 1 JRNL REVDAT 1 19-JAN-11 3Q5D 0 JRNL AUTH L.J.BYRNES,H.SONDERMANN JRNL TITL STRUCTURAL BASIS FOR THE NUCLEOTIDE-DEPENDENT DIMERIZATION JRNL TITL 2 OF THE LARGE G PROTEIN ATLASTIN-1/SPG3A. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 2216 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21220294 JRNL DOI 10.1073/PNAS.1012792108 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 31518 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3154 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.1347 - 7.6660 1.00 1334 145 0.1900 0.2303 REMARK 3 2 7.6660 - 6.0886 1.00 1326 148 0.1829 0.2315 REMARK 3 3 6.0886 - 5.3201 0.99 1327 141 0.1768 0.2568 REMARK 3 4 5.3201 - 4.8342 0.99 1311 142 0.1630 0.1879 REMARK 3 5 4.8342 - 4.4880 0.99 1317 150 0.1433 0.2109 REMARK 3 6 4.4880 - 4.2235 0.99 1313 146 0.1451 0.2157 REMARK 3 7 4.2235 - 4.0121 0.98 1295 138 0.1727 0.2354 REMARK 3 8 4.0121 - 3.8375 0.98 1285 148 0.1731 0.2410 REMARK 3 9 3.8375 - 3.6899 0.97 1298 147 0.1926 0.2205 REMARK 3 10 3.6899 - 3.5626 0.97 1290 141 0.2008 0.3044 REMARK 3 11 3.5626 - 3.4512 0.96 1274 142 0.1944 0.2311 REMARK 3 12 3.4512 - 3.3526 0.96 1258 148 0.2037 0.2640 REMARK 3 13 3.3526 - 3.2644 0.96 1259 144 0.1864 0.2604 REMARK 3 14 3.2644 - 3.1847 0.93 1254 131 0.2089 0.2968 REMARK 3 15 3.1847 - 3.1123 0.91 1219 134 0.2229 0.3495 REMARK 3 16 3.1123 - 3.0461 0.90 1192 131 0.2396 0.3626 REMARK 3 17 3.0461 - 2.9852 0.89 1161 137 0.2393 0.3388 REMARK 3 18 2.9852 - 2.9289 0.89 1176 130 0.2721 0.3127 REMARK 3 19 2.9289 - 2.8766 0.89 1178 141 0.2343 0.2973 REMARK 3 20 2.8766 - 2.8278 0.84 1095 128 0.2492 0.3132 REMARK 3 21 2.8278 - 2.7822 0.81 1078 117 0.2876 0.3944 REMARK 3 22 2.7822 - 2.7394 0.82 1087 109 0.3002 0.3876 REMARK 3 23 2.7394 - 2.6991 0.78 1037 116 0.3322 0.4650 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 60.44 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.17680 REMARK 3 B22 (A**2) : 4.17680 REMARK 3 B33 (A**2) : -8.35360 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3387 REMARK 3 ANGLE : 1.254 4576 REMARK 3 CHIRALITY : 0.090 499 REMARK 3 PLANARITY : 0.006 586 REMARK 3 DIHEDRAL : 20.433 1269 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (RESID 29:199) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9367 42.5440 46.1842 REMARK 3 T TENSOR REMARK 3 T11: 0.2104 T22: 0.3139 REMARK 3 T33: 0.2409 T12: 0.0720 REMARK 3 T13: 0.0366 T23: 0.0377 REMARK 3 L TENSOR REMARK 3 L11: 1.3668 L22: 2.7615 REMARK 3 L33: 1.7453 L12: 0.4859 REMARK 3 L13: 0.5757 L23: 0.2147 REMARK 3 S TENSOR REMARK 3 S11: 0.1721 S12: 0.0743 S13: 0.2636 REMARK 3 S21: -0.1363 S22: 0.0657 S23: 0.3448 REMARK 3 S31: -0.0956 S32: -0.5026 S33: -0.1939 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (RESID 200:341) REMARK 3 ORIGIN FOR THE GROUP (A): 14.2623 38.6792 50.0119 REMARK 3 T TENSOR REMARK 3 T11: 0.3492 T22: 0.3377 REMARK 3 T33: 0.2384 T12: -0.0246 REMARK 3 T13: -0.0610 T23: -0.0276 REMARK 3 L TENSOR REMARK 3 L11: 1.8903 L22: 1.1563 REMARK 3 L33: 1.1467 L12: 0.3850 REMARK 3 L13: -0.2629 L23: -1.0332 REMARK 3 S TENSOR REMARK 3 S11: 0.2799 S12: -0.4095 S13: 0.0318 REMARK 3 S21: 0.5341 S22: -0.0722 S23: -0.0701 REMARK 3 S31: 0.0387 S32: -0.1355 S33: -0.1743 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (RESID 342:438) REMARK 3 ORIGIN FOR THE GROUP (A): 46.8770 66.9100 25.1272 REMARK 3 T TENSOR REMARK 3 T11: 0.7320 T22: 0.5413 REMARK 3 T33: 0.2970 T12: -0.4046 REMARK 3 T13: -0.0075 T23: 0.0157 REMARK 3 L TENSOR REMARK 3 L11: 0.9299 L22: 1.8666 REMARK 3 L33: 3.5190 L12: 0.2279 REMARK 3 L13: -1.9225 L23: -1.1656 REMARK 3 S TENSOR REMARK 3 S11: 0.1960 S12: -0.4504 S13: -0.0348 REMARK 3 S21: 0.3752 S22: -0.3492 S23: 0.0483 REMARK 3 S31: -0.8983 S32: 0.9013 S33: 0.0781 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3Q5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063214. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33815 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE, PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE PH 8.5, 30% PEG-MME550, REMARK 280 0.1 M SUCCINIC ACID PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 69.44533 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 34.72267 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 52.08400 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 17.36133 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 86.80667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.44533 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 34.72267 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 17.36133 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 52.08400 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 86.80667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 69.44533 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 MSE A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 ASN A 4 REMARK 465 ARG A 5 REMARK 465 ARG A 6 REMARK 465 ASP A 7 REMARK 465 ARG A 8 REMARK 465 ASN A 9 REMARK 465 SER A 10 REMARK 465 TRP A 11 REMARK 465 GLY A 12 REMARK 465 GLY A 13 REMARK 465 PHE A 14 REMARK 465 SER A 15 REMARK 465 GLU A 16 REMARK 465 LYS A 17 REMARK 465 THR A 18 REMARK 465 TYR A 19 REMARK 465 GLU A 20 REMARK 465 TRP A 21 REMARK 465 SER A 22 REMARK 465 SER A 23 REMARK 465 GLU A 24 REMARK 465 GLU A 25 REMARK 465 GLU A 26 REMARK 465 GLU A 27 REMARK 465 PRO A 28 REMARK 465 LYS A 439 REMARK 465 ASN A 440 REMARK 465 ILE A 441 REMARK 465 PHE A 442 REMARK 465 HIS A 443 REMARK 465 ALA A 444 REMARK 465 ALA A 445 REMARK 465 ARG A 446 REMARK 465 THR A 447 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 VAL A 29 CG1 CG2 REMARK 470 LYS A 30 CG CD CE NZ REMARK 470 HIS A 247 CG ND1 CD2 CE1 NE2 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 O ASP A 98 N GLY A 101 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 VAL A 97 CB - CA - C ANGL. DEV. = -21.6 DEGREES 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 LYS A 31 179.78 -53.21 REMARK 500 ASP A 43 -1.25 -56.58 REMARK 500 VAL A 62 -29.54 -142.25 REMARK 500 VAL A 97 5.57 55.24 REMARK 500 TRP A 99 -38.63 -35.80 REMARK 500 TYR A 103 -24.66 -39.41 REMARK 500 SER A 116 84.66 -68.92 REMARK 500 SER A 153 154.13 176.87 REMARK 500 SER A 179 -79.15 -90.29 REMARK 500 ALA A 200 0.76 -67.36 REMARK 500 GLN A 210 -94.86 -93.93 REMARK 500 GLU A 248 -46.54 -137.90 REMARK 500 LEU A 250 42.28 -78.94 REMARK 500 GLN A 251 72.49 -100.50 REMARK 500 ASP A 283 14.21 -146.65 REMARK 500 CYS A 375 54.97 -112.86 REMARK 500 LYS A 379 -122.63 46.33 REMARK 500 PHE A 381 127.66 -36.35 REMARK 500 PRO A 384 -28.45 -39.08 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 A 448 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 81 OG REMARK 620 2 GDP A3850 O2B 77.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 3850 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 448 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3Q5E RELATED DB: PDB DBREF 3Q5D A 1 447 UNP Q8WXF7 ATLA1_HUMAN 1 447 SEQRES 1 A 447 MSE ALA LYS ASN ARG ARG ASP ARG ASN SER TRP GLY GLY SEQRES 2 A 447 PHE SER GLU LYS THR TYR GLU TRP SER SER GLU GLU GLU SEQRES 3 A 447 GLU PRO VAL LYS LYS ALA GLY PRO VAL GLN VAL LEU ILE SEQRES 4 A 447 VAL LYS ASP ASP HIS SER PHE GLU LEU ASP GLU THR ALA SEQRES 5 A 447 LEU ASN ARG ILE LEU LEU SER GLU ALA VAL ARG ASP LYS SEQRES 6 A 447 GLU VAL VAL ALA VAL SER VAL ALA GLY ALA PHE ARG LYS SEQRES 7 A 447 GLY LYS SER PHE LEU MSE ASP PHE MSE LEU ARG TYR MSE SEQRES 8 A 447 TYR ASN GLN GLU SER VAL ASP TRP VAL GLY ASP TYR ASN SEQRES 9 A 447 GLU PRO LEU THR GLY PHE SER TRP ARG GLY GLY SER GLU SEQRES 10 A 447 ARG GLU THR THR GLY ILE GLN ILE TRP SER GLU ILE PHE SEQRES 11 A 447 LEU ILE ASN LYS PRO ASP GLY LYS LYS VAL ALA VAL LEU SEQRES 12 A 447 LEU MSE ASP THR GLN GLY THR PHE ASP SER GLN SER THR SEQRES 13 A 447 LEU ARG ASP SER ALA THR VAL PHE ALA LEU SER THR MSE SEQRES 14 A 447 ILE SER SER ILE GLN VAL TYR ASN LEU SER GLN ASN VAL SEQRES 15 A 447 GLN GLU ASP ASP LEU GLN HIS LEU GLN LEU PHE THR GLU SEQRES 16 A 447 TYR GLY ARG LEU ALA MSE GLU GLU THR PHE LEU LYS PRO SEQRES 17 A 447 PHE GLN SER LEU ILE PHE LEU VAL ARG ASP TRP SER PHE SEQRES 18 A 447 PRO TYR GLU PHE SER TYR GLY ALA ASP GLY GLY ALA LYS SEQRES 19 A 447 PHE LEU GLU LYS ARG LEU LYS VAL SER GLY ASN GLN HIS SEQRES 20 A 447 GLU GLU LEU GLN ASN VAL ARG LYS HIS ILE HIS SER CYS SEQRES 21 A 447 PHE THR ASN ILE SER CYS PHE LEU LEU PRO HIS PRO GLY SEQRES 22 A 447 LEU LYS VAL ALA THR ASN PRO ASN PHE ASP GLY LYS LEU SEQRES 23 A 447 LYS GLU ILE ASP ASP GLU PHE ILE LYS ASN LEU LYS ILE SEQRES 24 A 447 LEU ILE PRO TRP LEU LEU SER PRO GLU SER LEU ASP ILE SEQRES 25 A 447 LYS GLU ILE ASN GLY ASN LYS ILE THR CYS ARG GLY LEU SEQRES 26 A 447 VAL GLU TYR PHE LYS ALA TYR ILE LYS ILE TYR GLN GLY SEQRES 27 A 447 GLU GLU LEU PRO HIS PRO LYS SER MSE LEU GLN ALA THR SEQRES 28 A 447 ALA GLU ALA ASN ASN LEU ALA ALA VAL ALA THR ALA LYS SEQRES 29 A 447 ASP THR TYR ASN LYS LYS MSE GLU GLU ILE CYS GLY GLY SEQRES 30 A 447 ASP LYS PRO PHE LEU ALA PRO ASN ASP LEU GLN THR LYS SEQRES 31 A 447 HIS LEU GLN LEU LYS GLU GLU SER VAL LYS LEU PHE ARG SEQRES 32 A 447 GLY VAL LYS LYS MSE GLY GLY GLU GLU PHE SER ARG ARG SEQRES 33 A 447 TYR LEU GLN GLN LEU GLU SER GLU ILE ASP GLU LEU TYR SEQRES 34 A 447 ILE GLN TYR ILE LYS HIS ASN ASP SER LYS ASN ILE PHE SEQRES 35 A 447 HIS ALA ALA ARG THR MODRES 3Q5D MSE A 84 MET SELENOMETHIONINE MODRES 3Q5D MSE A 87 MET SELENOMETHIONINE MODRES 3Q5D MSE A 91 MET SELENOMETHIONINE MODRES 3Q5D MSE A 145 MET SELENOMETHIONINE MODRES 3Q5D MSE A 169 MET SELENOMETHIONINE MODRES 3Q5D MSE A 201 MET SELENOMETHIONINE MODRES 3Q5D MSE A 347 MET SELENOMETHIONINE MODRES 3Q5D MSE A 371 MET SELENOMETHIONINE MODRES 3Q5D MSE A 408 MET SELENOMETHIONINE HET MSE A 84 8 HET MSE A 87 8 HET MSE A 91 8 HET MSE A 145 8 HET MSE A 169 8 HET MSE A 201 8 HET MSE A 347 8 HET MSE A 371 8 HET MSE A 408 8 HET GDP A3850 28 HET MG A 448 1 HETNAM MSE SELENOMETHIONINE HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 MSE 9(C5 H11 N O2 SE) FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 HOH *5(H2 O) HELIX 1 1 ASP A 49 LEU A 58 1 10 HELIX 2 2 GLY A 79 ASN A 93 1 15 HELIX 3 3 SER A 153 SER A 171 1 19 HELIX 4 4 GLN A 183 ALA A 200 1 18 HELIX 5 5 GLY A 228 VAL A 242 1 15 HELIX 6 6 ASN A 252 CYS A 260 1 9 HELIX 7 7 GLY A 273 ASN A 279 1 7 HELIX 8 8 LYS A 285 ILE A 289 5 5 HELIX 9 9 ASP A 290 SER A 306 1 17 HELIX 10 10 THR A 321 GLU A 339 1 19 HELIX 11 11 SER A 346 GLY A 376 1 31 HELIX 12 12 ALA A 383 ARG A 403 1 21 HELIX 13 13 GLY A 410 SER A 438 1 29 SHEET 1 A 5 PHE A 46 LEU A 48 0 SHEET 2 A 5 PRO A 34 VAL A 40 -1 N ILE A 39 O GLU A 47 SHEET 3 A 5 GLY A 122 TRP A 126 -1 O ILE A 123 N VAL A 37 SHEET 4 A 5 LYS A 139 GLN A 148 -1 O ASP A 146 N GLN A 124 SHEET 5 A 5 PHE A 130 ASN A 133 -1 N PHE A 130 O VAL A 142 SHEET 1 B 8 PHE A 46 LEU A 48 0 SHEET 2 B 8 PRO A 34 VAL A 40 -1 N ILE A 39 O GLU A 47 SHEET 3 B 8 GLY A 122 TRP A 126 -1 O ILE A 123 N VAL A 37 SHEET 4 B 8 LYS A 139 GLN A 148 -1 O ASP A 146 N GLN A 124 SHEET 5 B 8 VAL A 67 GLY A 74 1 N VAL A 68 O LEU A 143 SHEET 6 B 8 ILE A 173 LEU A 178 1 O VAL A 175 N SER A 71 SHEET 7 B 8 PHE A 209 TRP A 219 1 O ARG A 217 N LEU A 178 SHEET 8 B 8 PHE A 261 PRO A 270 1 O SER A 265 N PHE A 214 SHEET 1 C 2 GLU A 314 ILE A 315 0 SHEET 2 C 2 ASN A 318 LYS A 319 -1 O ASN A 318 N ILE A 315 LINK C LEU A 83 N MSE A 84 1555 1555 1.32 LINK C MSE A 84 N ASP A 85 1555 1555 1.33 LINK C PHE A 86 N MSE A 87 1555 1555 1.33 LINK C MSE A 87 N LEU A 88 1555 1555 1.33 LINK C TYR A 90 N MSE A 91 1555 1555 1.33 LINK C MSE A 91 N TYR A 92 1555 1555 1.33 LINK C LEU A 144 N MSE A 145 1555 1555 1.33 LINK C MSE A 145 N ASP A 146 1555 1555 1.32 LINK C THR A 168 N MSE A 169 1555 1555 1.33 LINK C MSE A 169 N ILE A 170 1555 1555 1.33 LINK C ALA A 200 N MSE A 201 1555 1555 1.33 LINK C MSE A 201 N GLU A 202 1555 1555 1.33 LINK C SER A 346 N MSE A 347 1555 1555 1.33 LINK C MSE A 347 N LEU A 348 1555 1555 1.33 LINK C LYS A 370 N MSE A 371 1555 1555 1.33 LINK C MSE A 371 N GLU A 372 1555 1555 1.33 LINK C LYS A 407 N MSE A 408 1555 1555 1.33 LINK C MSE A 408 N GLY A 409 1555 1555 1.32 LINK OG SER A 81 MG MG A 448 1555 1555 2.46 LINK O2B GDP A3850 MG MG A 448 1555 1555 2.52 CISPEP 1 SER A 243 GLY A 244 0 -4.21 CISPEP 2 GLY A 244 ASN A 245 0 -0.66 CISPEP 3 GLN A 246 HIS A 247 0 1.61 CISPEP 4 GLY A 376 GLY A 377 0 7.60 SITE 1 AC1 16 ARG A 77 LYS A 78 GLY A 79 LYS A 80 SITE 2 AC1 16 SER A 81 PHE A 82 GLN A 148 ARG A 217 SITE 3 AC1 16 ASP A 218 HIS A 271 PRO A 272 VAL A 276 SITE 4 AC1 16 ASN A 279 PRO A 280 MG A 448 HOH A 449 SITE 1 AC2 3 SER A 81 GLU A 117 GDP A3850 CRYST1 145.353 145.353 104.168 90.00 90.00 120.00 P 65 2 2 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 0.006880 0.003972 0.000000 0.00000 SCALE2 0.000000 0.007944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009600 0.00000