HEADER PROTEIN TRANSPORT 03-OCT-12 4BCX TITLE GAMMA 2 ADAPTIN EAR DOMAIN CRYSTAL STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EAR DOMAIN, RESIDUES 665-785; COMPND 5 SYNONYM: GAMMA2-ADAPTIN, G2AD; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: MODIFIED PRSETA KEYWDS PROTEIN TRANSPORT, GAE, GAMMA ADAPTIN EXPDTA X-RAY DIFFRACTION AUTHOR M.C.JUERGENS,J.VOROS,G.RAUTUREAU,D.SHEPHERD,V.E.PYE,J.MULDOON, AUTHOR 2 C.M.JOHNSON,A.ASHCROFT,S.M.V.FREUND,N.FERGUSON REVDAT 6 20-DEC-23 4BCX 1 REMARK REVDAT 5 12-JUL-17 4BCX 1 REVDAT 4 28-AUG-13 4BCX 1 JRNL REVDAT 3 24-JUL-13 4BCX 1 JRNL REVDAT 2 17-JUL-13 4BCX 1 JRNL REVDAT 1 10-JUL-13 4BCX 0 JRNL AUTH M.C.JURGENS,J.VOROS,G.J.P.RAUTUREAU,D.A.SHEPHERD,V.E.PYE, JRNL AUTH 2 J.MULDOON,C.M.JOHNSON,A.E.ASHCROFT,S.M.V.FREUND,N.FERGUSON JRNL TITL THE HEPATITIS B VIRUS PRES1 DOMAIN HIJACKS HOST TRAFFICKING JRNL TITL 2 PROTEINS BY MOTIF MIMICRY. JRNL REF NAT.CHEM.BIOL. V. 9 540 2013 JRNL REFN ISSN 1552-4450 JRNL PMID 23851574 JRNL DOI 10.1038/NCHEMBIO.1294 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 9859 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 475 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 26.5573 - 2.8837 1.00 3303 170 0.1816 0.2091 REMARK 3 2 2.8837 - 2.2893 0.98 3100 164 0.2300 0.2928 REMARK 3 3 2.2893 - 2.0000 0.96 2981 141 0.3362 0.3884 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.70 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 : 0.004 996 REMARK 3 ANGLE : 0.810 1357 REMARK 3 CHIRALITY : 0.044 156 REMARK 3 PLANARITY : 0.003 179 REMARK 3 DIHEDRAL : 11.989 378 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 20.5613 34.2909 38.3079 REMARK 3 T TENSOR REMARK 3 T11: 0.1612 T22: 0.1807 REMARK 3 T33: 0.1636 T12: 0.0063 REMARK 3 T13: -0.0096 T23: -0.0153 REMARK 3 L TENSOR REMARK 3 L11: 0.9313 L22: 1.5852 REMARK 3 L33: 2.5451 L12: 0.6896 REMARK 3 L13: -0.8933 L23: -1.5655 REMARK 3 S TENSOR REMARK 3 S11: 0.0190 S12: -0.0523 S13: 0.0213 REMARK 3 S21: -0.0615 S22: -0.0598 S23: -0.0650 REMARK 3 S31: -0.0445 S32: 0.1062 S33: 0.0427 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 4BCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1290053715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC VARIMAX HR OPTICS REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE DETECTOR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9894 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 26.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 11.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.14000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.20 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: PDB ENTRY 1P4U REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES/IMIDAZOLE BUFFER PH 6.5, REMARK 280 0.03 M EACH OF DI-, TRI-, TETRA- AND PENTA-ETHYLENEGLYCOL, 10% REMARK 280 (W/V) PEG 20000 AND 24% (V/V) PEG400 (USING A 2:1 RATIO OF REMARK 280 PROTEIN TO MOTHER LIQUOR) 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 17.62000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.11000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.83000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.11000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.62000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.83000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 662 REMARK 465 GLY A 663 REMARK 465 SER A 664 REMARK 465 ALA A 665 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 HOH A 2009 O HOH A 2089 2.18 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 PHE A 673 132.98 -172.07 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 IMD A 1786 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PDO A 1787 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YMT RELATED DB: PDB REMARK 900 GAMMA 2 ADAPTIN EAR DOMAIN CRYSTAL STRUCTURE WITH PHAGE PEPTIDE REMARK 900 GEEWGPWV DBREF 4BCX A 665 785 UNP O75843 AP1G2_HUMAN 665 785 SEQADV 4BCX GLY A 662 UNP O75843 EXPRESSION TAG SEQADV 4BCX GLY A 663 UNP O75843 EXPRESSION TAG SEQADV 4BCX SER A 664 UNP O75843 EXPRESSION TAG SEQRES 1 A 124 GLY GLY SER ALA PRO ILE PRO ASP LEU LYS VAL PHE GLU SEQRES 2 A 124 ARG GLU GLY VAL GLN LEU ASN LEU SER PHE ILE ARG PRO SEQRES 3 A 124 PRO GLU ASN PRO ALA LEU LEU LEU ILE THR ILE THR ALA SEQRES 4 A 124 THR ASN PHE SER GLU GLY ASP VAL THR HIS PHE ILE CYS SEQRES 5 A 124 GLN ALA ALA VAL PRO LYS SER LEU GLN LEU GLN LEU GLN SEQRES 6 A 124 ALA PRO SER GLY ASN THR VAL PRO ALA ARG GLY GLY LEU SEQRES 7 A 124 PRO ILE THR GLN LEU PHE ARG ILE LEU ASN PRO ASN LYS SEQRES 8 A 124 ALA PRO LEU ARG LEU LYS LEU ARG LEU THR TYR ASP HIS SEQRES 9 A 124 PHE HIS GLN SER VAL GLN GLU ILE PHE GLU VAL ASN ASN SEQRES 10 A 124 LEU PRO VAL GLU SER TRP GLN HET IMD A1786 5 HET PDO A1787 5 HETNAM IMD IMIDAZOLE HETNAM PDO 1,3-PROPANDIOL FORMUL 2 IMD C3 H5 N2 1+ FORMUL 3 PDO C3 H8 O2 FORMUL 4 HOH *110(H2 O) HELIX 1 1 PRO A 780 TRP A 784 5 5 SHEET 1 AA 5 LEU A 670 ARG A 675 0 SHEET 2 AA 5 VAL A 678 ILE A 685 -1 O VAL A 678 N ARG A 675 SHEET 3 AA 5 LEU A 693 ASN A 702 -1 O LEU A 695 N ILE A 685 SHEET 4 AA 5 ILE A 741 LEU A 748 -1 O ILE A 741 N ALA A 700 SHEET 5 AA 5 GLN A 722 LEU A 725 -1 O GLN A 722 N LEU A 748 SHEET 1 AB 3 VAL A 708 ALA A 716 0 SHEET 2 AB 3 LYS A 758 HIS A 765 -1 O LYS A 758 N ALA A 716 SHEET 3 AB 3 GLN A 768 GLU A 775 -1 O GLN A 768 N HIS A 765 SITE 1 AC1 3 ALA A 716 LYS A 758 GLU A 775 SITE 1 AC2 1 HOH A2110 CRYST1 35.240 37.660 106.220 90.00 90.00 90.00 P 21 21 21 4 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 0.028377 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009414 0.00000