HEADER ENDOCYTOSIS/EXOCYTOSIS 28-JAN-00 1EDU TITLE CRYSTAL STRUCTURE OF THE ENTH DOMAIN OF RAT EPSIN 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EH DOMAIN BINDING PROTEIN EPSIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL FRAGMENT; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 ORGAN: BRAIN; SOURCE 6 CELL: NEURON; SOURCE 7 EXPRESSION_SYSTEM: BACTERIA; SOURCE 8 EXPRESSION_SYSTEM_COMMON: EUBACTERIA; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 2; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEX6T-1 KEYWDS ALPHA-HELIX, ENDOCYTOSIS-EXOCYTOSIS COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.H.HYMAN,H.CHEN,P.DECAMILLI,A.T.BRUNGER REVDAT 5 06-NOV-24 1EDU 1 REMARK SEQADV LINK REVDAT 4 31-JAN-18 1EDU 1 REMARK REVDAT 3 24-FEB-09 1EDU 1 VERSN REVDAT 2 01-APR-03 1EDU 1 JRNL REVDAT 1 10-MAY-00 1EDU 0 JRNL AUTH J.HYMAN,H.CHEN,P.P.DI FIORE,P.DE CAMILLI,A.T.BRUNGER JRNL TITL EPSIN 1 UNDERGOES NUCLEOCYTOSOLIC SHUTTLING AND ITS EPS15 JRNL TITL 2 INTERACTOR NH(2)-TERMINAL HOMOLOGY (ENTH) DOMAIN, JRNL TITL 3 STRUCTURALLY SIMILAR TO ARMADILLO AND HEAT REPEATS, JRNL TITL 4 INTERACTS WITH THE TRANSCRIPTION FACTOR PROMYELOCYTIC JRNL TITL 5 LEUKEMIA ZN(2)+ FINGER PROTEIN (PLZF). JRNL REF J.CELL BIOL. V. 149 537 2000 JRNL REFN ISSN 0021-9525 JRNL PMID 10791968 JRNL DOI 10.1083/JCB.149.3.537 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : HUBER/ENGH REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 500.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 23618 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2241 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1210 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.93 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.058 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1000010473. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-99; 15-JUN-99; 15-JUN-99; REMARK 200 15-JUN-99 REMARK 200 TEMPERATURE (KELVIN) : 105; 105; 105; 105 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y; Y REMARK 200 RADIATION SOURCE : SSRL; SSRL; SSRL; SSRL REMARK 200 BEAMLINE : BL1-5; BL1-5; BL1-5; BL1-5 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL; NULL; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.06883; 0.97984; 0.97961; REMARK 200 0.92526 REMARK 200 MONOCHROMATOR : NULL; NULL; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD; CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; ADSC QUANTUM 4; REMARK 200 ADSC QUANTUM 4; ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24057 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL; NULL; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, NA-HEPES, ETHYLENE GLYCOL, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 20K, REMARK 280 TEMPERATURE 293.0K 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 33.32233 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 66.64467 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 66.64467 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 33.32233 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 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 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 HIS A 5 -101.91 -81.04 REMARK 500 PRO A 22 46.26 -67.98 REMARK 500 TYR A 101 112.80 -167.54 REMARK 500 THR A 149 -147.91 -61.83 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 EDO A 788 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 789 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 793 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 794 DBREF 1EDU A 2 150 UNP O88339 EPN1_RAT 12 160 SEQADV 1EDU MSE A 30 UNP O88339 MET 40 MODIFIED RESIDUE SEQADV 1EDU MSE A 47 UNP O88339 MET 57 MODIFIED RESIDUE SEQADV 1EDU MSE A 49 UNP O88339 MET 59 MODIFIED RESIDUE SEQADV 1EDU MSE A 68 UNP O88339 MET 78 MODIFIED RESIDUE SEQADV 1EDU MSE A 71 UNP O88339 MET 81 MODIFIED RESIDUE SEQADV 1EDU MSE A 90 UNP O88339 MET 100 MODIFIED RESIDUE SEQRES 1 A 149 ASN ILE VAL HIS ASN TYR SER GLU ALA GLU ILE LYS VAL SEQRES 2 A 149 ARG GLU ALA THR SER ASN ASP PRO TRP GLY PRO SER SER SEQRES 3 A 149 SER LEU MSE SER GLU ILE ALA ASP LEU THR TYR ASN VAL SEQRES 4 A 149 VAL ALA PHE SER GLU ILE MSE SER MSE ILE TRP LYS ARG SEQRES 5 A 149 LEU ASN ASP HIS GLY LYS ASN TRP ARG HIS VAL TYR LYS SEQRES 6 A 149 ALA MSE THR LEU MSE GLU TYR LEU ILE LYS THR GLY SER SEQRES 7 A 149 GLU ARG VAL SER GLN GLN CYS LYS GLU ASN MSE TYR ALA SEQRES 8 A 149 VAL GLN THR LEU LYS ASP PHE GLN TYR VAL ASP ARG ASP SEQRES 9 A 149 GLY LYS ASP GLN GLY VAL ASN VAL ARG GLU LYS ALA LYS SEQRES 10 A 149 GLN LEU VAL ALA LEU LEU ARG ASP GLU ASP ARG LEU ARG SEQRES 11 A 149 GLU GLU ARG ALA HIS ALA LEU LYS THR LYS GLU LYS LEU SEQRES 12 A 149 ALA GLN THR ALA THR ALA MODRES 1EDU MSE A 30 MET SELENOMETHIONINE MODRES 1EDU MSE A 47 MET SELENOMETHIONINE MODRES 1EDU MSE A 49 MET SELENOMETHIONINE MODRES 1EDU MSE A 68 MET SELENOMETHIONINE MODRES 1EDU MSE A 71 MET SELENOMETHIONINE MODRES 1EDU MSE A 90 MET SELENOMETHIONINE HET MSE A 30 8 HET MSE A 47 8 HET MSE A 49 8 HET MSE A 68 8 HET MSE A 71 8 HET MSE A 90 8 HET EDO A 788 4 HET EDO A 789 4 HET EDO A 793 4 HET EDO A 794 4 HETNAM MSE SELENOMETHIONINE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 EDO 4(C2 H6 O2) FORMUL 6 HOH *63(H2 O) HELIX 1 1 SER A 8 THR A 18 1 11 HELIX 2 2 SER A 26 THR A 37 1 12 HELIX 3 3 ASN A 39 ASN A 55 1 17 HELIX 4 4 HIS A 57 LYS A 59 5 3 HELIX 5 5 ASN A 60 GLY A 78 1 19 HELIX 6 6 SER A 79 ASN A 89 1 11 HELIX 7 7 ASN A 89 THR A 95 1 7 HELIX 8 8 LEU A 96 PHE A 99 5 4 HELIX 9 9 GLN A 109 ASP A 126 1 18 HELIX 10 10 ASP A 126 GLN A 146 1 21 LINK C LEU A 29 N MSE A 30 1555 1555 1.33 LINK C MSE A 30 N SER A 31 1555 1555 1.33 LINK C ILE A 46 N MSE A 47 1555 1555 1.33 LINK C MSE A 47 N SER A 48 1555 1555 1.33 LINK C SER A 48 N MSE A 49 1555 1555 1.33 LINK C MSE A 49 N ILE A 50 1555 1555 1.33 LINK C ALA A 67 N MSE A 68 1555 1555 1.33 LINK C MSE A 68 N THR A 69 1555 1555 1.33 LINK C LEU A 70 N MSE A 71 1555 1555 1.33 LINK C MSE A 71 N GLU A 72 1555 1555 1.33 LINK C ASN A 89 N MSE A 90 1555 1555 1.33 LINK C MSE A 90 N TYR A 91 1555 1555 1.33 SITE 1 AC1 6 TYR A 38 GLU A 72 LYS A 76 LEU A 123 SITE 2 AC1 6 ARG A 129 GLU A 133 SITE 1 AC2 6 GLY A 106 LYS A 107 ASP A 108 ALA A 135 SITE 2 AC2 6 HIS A 136 LYS A 139 SITE 1 AC3 3 GLU A 115 LEU A 138 GLU A 142 SITE 1 AC4 6 ASP A 21 TRP A 23 GLY A 24 ARG A 62 SITE 2 AC4 6 TYR A 65 HOH A 847 CRYST1 49.807 49.807 99.967 90.00 90.00 120.00 P 31 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020077 0.011592 0.000000 0.00000 SCALE2 0.000000 0.023183 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010003 0.00000