HEADER HYDROLASE 06-AUG-15 5D3Q TITLE DYNAMIN 1 GTPASE-BSE FUSION DIMER COMPLEXED WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DYNAMIN-1,DYNAMIN-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 5-320, 726-746,UNP RESIDUES 5-320, 726-746; COMPND 5 EC: 3.6.5.5,3.6.5.5; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: THE SEQUENCE CONTAINS RESIDUES 5-320 AND 726-746 OF COMPND 8 HUMAN DYNAMIN 1. THE VERY N-TERMINUS CONTAINS A GLYCINE RESIDUE FROM COMPND 9 THE TEV CLEAVAGE STEP. THE TWO DYNAMIN FRAGMENTS ARE CONNECTED BY A COMPND 10 LINKER SEQUENCE OF EIGHT RESIDUES (KHGTDSRV). SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DNM1, DNM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HYDROLASE, FUSION PROTEIN, GTPASE, ENDOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR R.ANAND,S.ESCHENBURG,T.F.REUBOLD REVDAT 4 10-JAN-24 5D3Q 1 REMARK REVDAT 3 22-MAR-17 5D3Q 1 REMARK REVDAT 2 14-SEP-16 5D3Q 1 JRNL REVDAT 1 02-DEC-15 5D3Q 0 JRNL AUTH R.ANAND,S.ESCHENBURG,T.F.REUBOLD JRNL TITL CRYSTAL STRUCTURE OF THE GTPASE DOMAIN AND THE BUNDLE JRNL TITL 2 SIGNALLING ELEMENT OF DYNAMIN IN THE GDP STATE. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 469 76 2016 JRNL REFN ESSN 1090-2104 JRNL PMID 26612256 JRNL DOI 10.1016/J.BBRC.2015.11.074 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 72207 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3611 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 47.6447 - 5.0343 1.00 2705 143 0.1682 0.1793 REMARK 3 2 5.0343 - 3.9965 1.00 2683 141 0.1467 0.1696 REMARK 3 3 3.9965 - 3.4915 1.00 2720 143 0.1573 0.1684 REMARK 3 4 3.4915 - 3.1724 1.00 2658 140 0.1739 0.1883 REMARK 3 5 3.1724 - 2.9450 1.00 2702 143 0.1811 0.2215 REMARK 3 6 2.9450 - 2.7714 1.00 2673 140 0.1782 0.2209 REMARK 3 7 2.7714 - 2.6326 1.00 2691 142 0.1771 0.2129 REMARK 3 8 2.6326 - 2.5180 0.99 2709 142 0.1740 0.2332 REMARK 3 9 2.5180 - 2.4211 0.98 2639 139 0.1722 0.2227 REMARK 3 10 2.4211 - 2.3376 0.97 2620 138 0.1781 0.2176 REMARK 3 11 2.3376 - 2.2645 0.97 2661 140 0.1741 0.2189 REMARK 3 12 2.2645 - 2.1997 0.98 2608 137 0.1778 0.2229 REMARK 3 13 2.1997 - 2.1418 0.97 2653 140 0.1765 0.2043 REMARK 3 14 2.1418 - 2.0896 0.97 2596 137 0.1755 0.2185 REMARK 3 15 2.0896 - 2.0421 0.97 2644 139 0.1826 0.2240 REMARK 3 16 2.0421 - 1.9986 0.97 2579 136 0.1813 0.2324 REMARK 3 17 1.9986 - 1.9586 0.97 2657 140 0.1781 0.2385 REMARK 3 18 1.9586 - 1.9217 0.96 2538 133 0.1795 0.1879 REMARK 3 19 1.9217 - 1.8874 0.97 2690 142 0.1819 0.2318 REMARK 3 20 1.8874 - 1.8554 0.97 2552 134 0.1810 0.2159 REMARK 3 21 1.8554 - 1.8254 0.96 2620 138 0.1838 0.2567 REMARK 3 22 1.8254 - 1.7973 0.96 2616 138 0.1947 0.2325 REMARK 3 23 1.7973 - 1.7709 0.96 2599 136 0.1964 0.2471 REMARK 3 24 1.7709 - 1.7460 0.96 2603 137 0.2012 0.2468 REMARK 3 25 1.7460 - 1.7224 0.96 2538 134 0.2105 0.2588 REMARK 3 26 1.7224 - 1.7000 0.96 2642 139 0.2069 0.2657 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.700 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) : 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 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 : 0.015 5347 REMARK 3 ANGLE : 1.400 7259 REMARK 3 CHIRALITY : 0.082 844 REMARK 3 PLANARITY : 0.008 945 REMARK 3 DIHEDRAL : 13.658 3346 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5D3Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212601. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72213 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 47.626 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 4.630 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : 0.10800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.85 REMARK 200 R MERGE FOR SHELL (I) : 0.24500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.700 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: 2X2E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BEFORE CRYSTALLIZATION SET-UPS, GG1 AT REMARK 280 A CONCENTRATION OF 10 MG/ML WAS SUPPLEMENTED WITH 2 MM GDP AND 2 REMARK 280 MM MGCL2 AND INCUBATED FOR 1 H ON ICE. GG1GDP WAS CRYSTALLIZED REMARK 280 BY HANGING DROP VAPOUR DIFFUSION MIXING 1.5 UL PROTEIN SOLUTION REMARK 280 WITH 1.5 UL RESERVOIR SOLUTION CONTAINING 0.1 M TRIS (PH 8.0), REMARK 280 26 % PEG 3350 AND 0.2 M NASCN. THE DROPS WERE EQUILIBRATED REMARK 280 AGAINST 700 UL OF RESERVOIR., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 710 REMARK 465 TYR A 711 REMARK 465 LYS A 712 REMARK 465 ASN A 713 REMARK 465 PHE A 714 REMARK 465 ARG A 715 REMARK 465 PRO A 716 REMARK 465 ASP A 717 REMARK 465 LYS A 718 REMARK 465 HIS A 719 REMARK 465 GLY A 720 REMARK 465 THR A 721 REMARK 465 ASP A 722 REMARK 465 SER A 723 REMARK 465 ASP A 744 REMARK 465 ILE A 745 REMARK 465 ASN A 746 REMARK 465 VAL B 108 REMARK 465 THR B 109 REMARK 465 GLY B 110 REMARK 465 THR B 111 REMARK 465 ASN B 112 REMARK 465 LYS B 113 REMARK 465 GLY B 114 REMARK 465 PHE B 317 REMARK 465 ARG B 318 REMARK 465 PRO B 319 REMARK 465 ASP B 320 REMARK 465 LYS B 321 REMARK 465 HIS B 322 REMARK 465 GLY B 323 REMARK 465 THR B 324 REMARK 465 ILE B 745 REMARK 465 ASN B 746 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 OG SER B 46 O1A GDP B 801 1.71 REMARK 500 NZ LYS A 90 O HOH A 901 1.97 REMARK 500 NH2 ARG A 157 OE2 GLU A 192 2.06 REMARK 500 O HOH A 1050 O HOH A 1179 2.11 REMARK 500 OD1 ASP B 247 O HOH B 902 2.13 REMARK 500 O HOH A 913 O HOH A 1131 2.16 REMARK 500 NH2 ARG A 54 CD GLU A 79 2.16 REMARK 500 NH2 ARG A 271 O HOH A 902 2.17 REMARK 500 O HOH B 1150 O HOH B 1161 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 909 O HOH B 1025 1565 2.03 REMARK 500 O HOH A 1127 O HOH B 1145 1455 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER B 46 CB SER B 46 OG 0.098 REMARK 500 ARG B 107 CD ARG B 107 NE -0.145 REMARK 500 ARG B 107 NE ARG B 107 CZ -0.180 REMARK 500 ARG B 107 CZ ARG B 107 NH1 -0.150 REMARK 500 ARG B 107 CZ ARG B 107 NH2 -0.140 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 LEU A 29 CA - CB - CG ANGL. DEV. = -19.6 DEGREES REMARK 500 LEU B 29 CA - CB - CG ANGL. DEV. = -23.2 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 ASN A 26 -57.49 -162.01 REMARK 500 PHE A 56 -3.14 -152.90 REMARK 500 ASN A 178 38.71 -90.97 REMARK 500 ASN B 26 -59.39 -164.24 REMARK 500 PHE B 56 -4.62 -156.56 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 GDP A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP B 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 802 DBREF 5D3Q A 5 717 UNP Q05193 DYN1_HUMAN 5 320 DBREF 5D3Q A 726 746 UNP Q05193 DYN1_HUMAN 726 746 DBREF 5D3Q B 5 320 UNP Q05193 DYN1_HUMAN 5 320 DBREF 5D3Q B 726 746 UNP Q05193 DYN1_HUMAN 726 746 SEQADV 5D3Q LYS A 718 UNP Q05193 LINKER SEQADV 5D3Q HIS A 719 UNP Q05193 LINKER SEQADV 5D3Q GLY A 720 UNP Q05193 LINKER SEQADV 5D3Q THR A 721 UNP Q05193 LINKER SEQADV 5D3Q ASP A 722 UNP Q05193 LINKER SEQADV 5D3Q SER A 723 UNP Q05193 LINKER SEQADV 5D3Q ARG A 724 UNP Q05193 LINKER SEQADV 5D3Q VAL A 725 UNP Q05193 LINKER SEQADV 5D3Q LYS B 321 UNP Q05193 LINKER SEQADV 5D3Q HIS B 322 UNP Q05193 LINKER SEQADV 5D3Q GLY B 323 UNP Q05193 LINKER SEQADV 5D3Q THR B 324 UNP Q05193 LINKER SEQADV 5D3Q ASP B 325 UNP Q05193 LINKER SEQADV 5D3Q SER B 326 UNP Q05193 LINKER SEQADV 5D3Q ARG B 724 UNP Q05193 LINKER SEQADV 5D3Q VAL B 725 UNP Q05193 LINKER SEQRES 1 A 345 GLY MET GLU ASP LEU ILE PRO LEU VAL ASN ARG LEU GLN SEQRES 2 A 345 ASP ALA PHE SER ALA ILE GLY GLN ASN ALA ASP LEU ASP SEQRES 3 A 345 LEU PRO GLN ILE ALA VAL VAL GLY GLY GLN SER ALA GLY SEQRES 4 A 345 LYS SER SER VAL LEU GLU ASN PHE VAL GLY ARG ASP PHE SEQRES 5 A 345 LEU PRO ARG GLY SER GLY ILE VAL THR ARG ARG PRO LEU SEQRES 6 A 345 VAL LEU GLN LEU VAL ASN ALA THR THR GLU TYR ALA GLU SEQRES 7 A 345 PHE LEU HIS CYS LYS GLY LYS LYS PHE THR ASP PHE GLU SEQRES 8 A 345 GLU VAL ARG LEU GLU ILE GLU ALA GLU THR ASP ARG VAL SEQRES 9 A 345 THR GLY THR ASN LYS GLY ILE SER PRO VAL PRO ILE ASN SEQRES 10 A 345 LEU ARG VAL TYR SER PRO HIS VAL LEU ASN LEU THR LEU SEQRES 11 A 345 VAL ASP LEU PRO GLY MET THR LYS VAL PRO VAL GLY ASP SEQRES 12 A 345 GLN PRO PRO ASP ILE GLU PHE GLN ILE ARG ASP MET LEU SEQRES 13 A 345 MET GLN PHE VAL THR LYS GLU ASN CYS LEU ILE LEU ALA SEQRES 14 A 345 VAL SER PRO ALA ASN SER ASP LEU ALA ASN SER ASP ALA SEQRES 15 A 345 LEU LYS VAL ALA LYS GLU VAL ASP PRO GLN GLY GLN ARG SEQRES 16 A 345 THR ILE GLY VAL ILE THR LYS LEU ASP LEU MET ASP GLU SEQRES 17 A 345 GLY THR ASP ALA ARG ASP VAL LEU GLU ASN LYS LEU LEU SEQRES 18 A 345 PRO LEU ARG ARG GLY TYR ILE GLY VAL VAL ASN ARG SER SEQRES 19 A 345 GLN LYS ASP ILE ASP GLY LYS LYS ASP ILE THR ALA ALA SEQRES 20 A 345 LEU ALA ALA GLU ARG LYS PHE PHE LEU SER HIS PRO SER SEQRES 21 A 345 TYR ARG HIS LEU ALA ASP ARG MET GLY THR PRO TYR LEU SEQRES 22 A 345 GLN LYS VAL LEU ASN GLN GLN LEU THR ASN HIS ILE ARG SEQRES 23 A 345 ASP THR LEU PRO GLY LEU ARG ASN LYS LEU GLN SER GLN SEQRES 24 A 345 LEU LEU SER ILE GLU LYS GLU VAL GLU GLU TYR LYS ASN SEQRES 25 A 345 PHE ARG PRO ASP LYS HIS GLY THR ASP SER ARG VAL ASP SEQRES 26 A 345 GLU MET LEU ARG MET TYR HIS ALA LEU LYS GLU ALA LEU SEQRES 27 A 345 SER ILE ILE GLY ASP ILE ASN SEQRES 1 B 345 GLY MET GLU ASP LEU ILE PRO LEU VAL ASN ARG LEU GLN SEQRES 2 B 345 ASP ALA PHE SER ALA ILE GLY GLN ASN ALA ASP LEU ASP SEQRES 3 B 345 LEU PRO GLN ILE ALA VAL VAL GLY GLY GLN SER ALA GLY SEQRES 4 B 345 LYS SER SER VAL LEU GLU ASN PHE VAL GLY ARG ASP PHE SEQRES 5 B 345 LEU PRO ARG GLY SER GLY ILE VAL THR ARG ARG PRO LEU SEQRES 6 B 345 VAL LEU GLN LEU VAL ASN ALA THR THR GLU TYR ALA GLU SEQRES 7 B 345 PHE LEU HIS CYS LYS GLY LYS LYS PHE THR ASP PHE GLU SEQRES 8 B 345 GLU VAL ARG LEU GLU ILE GLU ALA GLU THR ASP ARG VAL SEQRES 9 B 345 THR GLY THR ASN LYS GLY ILE SER PRO VAL PRO ILE ASN SEQRES 10 B 345 LEU ARG VAL TYR SER PRO HIS VAL LEU ASN LEU THR LEU SEQRES 11 B 345 VAL ASP LEU PRO GLY MET THR LYS VAL PRO VAL GLY ASP SEQRES 12 B 345 GLN PRO PRO ASP ILE GLU PHE GLN ILE ARG ASP MET LEU SEQRES 13 B 345 MET GLN PHE VAL THR LYS GLU ASN CYS LEU ILE LEU ALA SEQRES 14 B 345 VAL SER PRO ALA ASN SER ASP LEU ALA ASN SER ASP ALA SEQRES 15 B 345 LEU LYS VAL ALA LYS GLU VAL ASP PRO GLN GLY GLN ARG SEQRES 16 B 345 THR ILE GLY VAL ILE THR LYS LEU ASP LEU MET ASP GLU SEQRES 17 B 345 GLY THR ASP ALA ARG ASP VAL LEU GLU ASN LYS LEU LEU SEQRES 18 B 345 PRO LEU ARG ARG GLY TYR ILE GLY VAL VAL ASN ARG SER SEQRES 19 B 345 GLN LYS ASP ILE ASP GLY LYS LYS ASP ILE THR ALA ALA SEQRES 20 B 345 LEU ALA ALA GLU ARG LYS PHE PHE LEU SER HIS PRO SER SEQRES 21 B 345 TYR ARG HIS LEU ALA ASP ARG MET GLY THR PRO TYR LEU SEQRES 22 B 345 GLN LYS VAL LEU ASN GLN GLN LEU THR ASN HIS ILE ARG SEQRES 23 B 345 ASP THR LEU PRO GLY LEU ARG ASN LYS LEU GLN SER GLN SEQRES 24 B 345 LEU LEU SER ILE GLU LYS GLU VAL GLU GLU TYR LYS ASN SEQRES 25 B 345 PHE ARG PRO ASP LYS HIS GLY THR ASP SER ARG VAL ASP SEQRES 26 B 345 GLU MET LEU ARG MET TYR HIS ALA LEU LYS GLU ALA LEU SEQRES 27 B 345 SER ILE ILE GLY ASP ILE ASN HET GDP A 801 28 HET EDO A 802 4 HET GDP B 801 28 HET EDO B 802 4 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 GDP 2(C10 H15 N5 O11 P2) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 7 HOH *609(H2 O) HELIX 1 AA1 ASP A 8 ALA A 22 1 15 HELIX 2 AA2 ASN A 26 ASP A 30 5 5 HELIX 3 AA3 GLY A 43 GLY A 53 1 11 HELIX 4 AA4 ASP A 93 GLY A 110 1 18 HELIX 5 AA5 ASP A 151 THR A 165 1 15 HELIX 6 AA6 ASP A 180 ASN A 183 5 4 HELIX 7 AA7 SER A 184 ASP A 194 1 11 HELIX 8 AA8 LYS A 206 MET A 210 5 5 HELIX 9 AA9 ALA A 216 GLU A 221 1 6 HELIX 10 AB1 SER A 238 GLY A 244 1 7 HELIX 11 AB2 ASP A 247 HIS A 262 1 16 HELIX 12 AB3 TYR A 265 MET A 272 5 8 HELIX 13 AB4 GLY A 273 GLU A 312 1 40 HELIX 14 AB5 VAL A 725 GLY A 743 1 19 HELIX 15 AB6 GLY B 5 GLU B 7 5 3 HELIX 16 AB7 ASP B 8 ILE B 23 1 16 HELIX 17 AB8 ASN B 26 ASP B 30 5 5 HELIX 18 AB9 GLY B 43 GLY B 53 1 11 HELIX 19 AC1 ASP B 93 ARG B 107 1 15 HELIX 20 AC2 ASP B 151 THR B 165 1 15 HELIX 21 AC3 ASP B 180 ASN B 183 5 4 HELIX 22 AC4 SER B 184 ASP B 194 1 11 HELIX 23 AC5 LYS B 206 MET B 210 5 5 HELIX 24 AC6 ALA B 216 GLU B 221 1 6 HELIX 25 AC7 SER B 238 GLY B 244 1 7 HELIX 26 AC8 ASP B 247 HIS B 262 1 16 HELIX 27 AC9 TYR B 265 MET B 272 5 8 HELIX 28 AD1 GLY B 273 GLU B 313 1 41 HELIX 29 AD2 SER B 326 ASP B 744 1 22 SHEET 1 AA1 8 TYR A 80 PHE A 83 0 SHEET 2 AA1 8 ILE A 120 SER A 126 -1 O TYR A 125 N TYR A 80 SHEET 3 AA1 8 LEU A 69 ASN A 75 1 N VAL A 70 O ILE A 120 SHEET 4 AA1 8 LEU A 132 ASP A 136 -1 O LEU A 132 N LEU A 73 SHEET 5 AA1 8 GLN A 33 GLY A 38 1 N ILE A 34 O VAL A 135 SHEET 6 AA1 8 CYS A 169 PRO A 176 1 O LEU A 172 N ALA A 35 SHEET 7 AA1 8 THR A 200 THR A 205 1 O ILE A 201 N ILE A 171 SHEET 8 AA1 8 TYR A 231 GLY A 233 1 O ILE A 232 N GLY A 202 SHEET 1 AA2 8 TYR B 80 PHE B 83 0 SHEET 2 AA2 8 ILE B 120 SER B 126 -1 O TYR B 125 N TYR B 80 SHEET 3 AA2 8 LEU B 69 ASN B 75 1 N VAL B 70 O ILE B 120 SHEET 4 AA2 8 LEU B 132 ASP B 136 -1 O LEU B 132 N LEU B 73 SHEET 5 AA2 8 GLN B 33 GLY B 38 1 N ILE B 34 O VAL B 135 SHEET 6 AA2 8 CYS B 169 PRO B 176 1 O LEU B 172 N ALA B 35 SHEET 7 AA2 8 THR B 200 THR B 205 1 O ILE B 201 N ILE B 171 SHEET 8 AA2 8 TYR B 231 GLY B 233 1 O ILE B 232 N ILE B 204 SITE 1 AC1 22 SER A 41 ALA A 42 GLY A 43 LYS A 44 SITE 2 AC1 22 SER A 45 SER A 46 ARG A 59 LYS A 206 SITE 3 AC1 22 ASP A 208 LEU A 209 VAL A 235 ASN A 236 SITE 4 AC1 22 ARG A 237 SER A 238 GLN A 239 ILE A 242 SITE 5 AC1 22 EDO A 802 HOH A 912 HOH A 964 HOH A1099 SITE 6 AC1 22 ASP B 211 HOH B 974 SITE 1 AC2 5 SER A 45 PRO A 58 ARG A 59 GDP A 801 SITE 2 AC2 5 HOH A1009 SITE 1 AC3 22 ASP A 211 HOH A 987 SER B 41 ALA B 42 SITE 2 AC3 22 GLY B 43 LYS B 44 SER B 45 SER B 46 SITE 3 AC3 22 ARG B 59 LYS B 206 ASP B 208 LEU B 209 SITE 4 AC3 22 VAL B 235 ASN B 236 ARG B 237 SER B 238 SITE 5 AC3 22 GLN B 239 HOH B 916 HOH B1009 HOH B1073 SITE 6 AC3 22 HOH B1077 HOH B1102 SITE 1 AC4 5 LEU B 207 ASP B 208 MET B 210 HIS B 262 SITE 2 AC4 5 HOH B 940 CRYST1 44.220 49.960 82.520 99.40 87.18 105.18 P 1 2 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 0.022614 0.006136 -0.000157 0.00000 SCALE2 0.000000 0.020740 0.003276 0.00000 SCALE3 0.000000 0.000000 0.012283 0.00000