HEADER PROTEIN TRANSPORT 23-OCT-15 5AZW TITLE CRYSTAL STRUCTURE OF P24BETA1 GOLD DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSMEMBRANE EMP24 DOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MEMBRANE PROTEIN P24A,P24,P24 FAMILY PROTEIN BETA-1, COMPND 5 P24BETA1; 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 GENE: TMED2, RNP24; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN TRANSPORT, GPI-ANCHORED PROTEIN, P24 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.NAGAE,Y.YAMAGUCHI REVDAT 3 26-FEB-20 5AZW 1 JRNL REMARK REVDAT 2 19-OCT-16 5AZW 1 JRNL REVDAT 1 14-SEP-16 5AZW 0 JRNL AUTH M.NAGAE,T.HIRATA,K.MORITA-MATSUMOTO,R.THEILER,M.FUJITA, JRNL AUTH 2 T.KINOSHITA,Y.YAMAGUCHI JRNL TITL 3D STRUCTURE AND INTERACTION OF P24 BETA AND P24 DELTA GOLGI JRNL TITL 2 DYNAMICS DOMAINS: IMPLICATION FOR P24 COMPLEX FORMATION AND JRNL TITL 3 CARGO TRANSPORT JRNL REF J.MOL.BIOL. V. 428 4087 2016 JRNL REFN ESSN 1089-8638 JRNL PMID 27569046 JRNL DOI 10.1016/J.JMB.2016.08.023 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 26761 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1344 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 24.1397 - 3.2294 0.95 2495 146 0.1994 0.2076 REMARK 3 2 3.2294 - 2.5642 1.00 2570 155 0.2278 0.2416 REMARK 3 3 2.5642 - 2.2403 1.00 2543 141 0.2471 0.2466 REMARK 3 4 2.2403 - 2.0356 1.00 2574 131 0.2208 0.2684 REMARK 3 5 2.0356 - 1.8897 1.00 2534 127 0.2193 0.2269 REMARK 3 6 1.8897 - 1.7784 1.00 2558 136 0.2213 0.2040 REMARK 3 7 1.7784 - 1.6893 1.00 2521 131 0.2336 0.2331 REMARK 3 8 1.6893 - 1.6158 1.00 2540 122 0.2261 0.2321 REMARK 3 9 1.6158 - 1.5536 1.00 2530 126 0.2372 0.2923 REMARK 3 10 1.5536 - 1.5000 0.99 2552 129 0.2483 0.2963 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.670 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 : 0.007 1498 REMARK 3 ANGLE : 0.969 2007 REMARK 3 CHIRALITY : 0.061 212 REMARK 3 PLANARITY : 0.006 257 REMARK 3 DIHEDRAL : 9.464 873 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 5AZW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1300000291. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR 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 : 26802 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 79.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.34600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL (PH 8.5), 0.2 M SODIUM REMARK 280 CHLORIDE AND 25 % (W/V) PEG 3,350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 48.88600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.83200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.88600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.83200 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 312 LIES ON A SPECIAL POSITION. 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 SER A 19 REMARK 465 GLU A 114 REMARK 465 SER B 19 REMARK 465 GLY B 20 REMARK 465 GLU B 114 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 OD2 ASP A 65 NZ LYS A 67 1.99 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AZX RELATED DB: PDB REMARK 900 RELATED ID: 5AZY RELATED DB: PDB DBREF 5AZW A 19 114 UNP Q15363 TMED2_HUMAN 19 114 DBREF 5AZW B 19 114 UNP Q15363 TMED2_HUMAN 19 114 SEQRES 1 A 96 SER GLY TYR PHE VAL SER ILE ASP ALA HIS ALA GLU GLU SEQRES 2 A 96 CYS PHE PHE GLU ARG VAL THR SER GLY THR LYS MET GLY SEQRES 3 A 96 LEU ILE PHE GLU VAL ALA GLU GLY GLY PHE LEU ASP ILE SEQRES 4 A 96 ASP VAL GLU ILE THR GLY PRO ASP ASN LYS GLY ILE TYR SEQRES 5 A 96 LYS GLY ASP ARG GLU SER SER GLY LYS TYR THR PHE ALA SEQRES 6 A 96 ALA HIS MET ASP GLY THR TYR LYS PHE CYS PHE SER ASN SEQRES 7 A 96 ARG MET SER THR MET THR PRO LYS ILE VAL MET PHE THR SEQRES 8 A 96 ILE ASP ILE GLY GLU SEQRES 1 B 96 SER GLY TYR PHE VAL SER ILE ASP ALA HIS ALA GLU GLU SEQRES 2 B 96 CYS PHE PHE GLU ARG VAL THR SER GLY THR LYS MET GLY SEQRES 3 B 96 LEU ILE PHE GLU VAL ALA GLU GLY GLY PHE LEU ASP ILE SEQRES 4 B 96 ASP VAL GLU ILE THR GLY PRO ASP ASN LYS GLY ILE TYR SEQRES 5 B 96 LYS GLY ASP ARG GLU SER SER GLY LYS TYR THR PHE ALA SEQRES 6 B 96 ALA HIS MET ASP GLY THR TYR LYS PHE CYS PHE SER ASN SEQRES 7 B 96 ARG MET SER THR MET THR PRO LYS ILE VAL MET PHE THR SEQRES 8 B 96 ILE ASP ILE GLY GLU HET EDO A 201 4 HET EDO B 201 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 HOH *55(H2 O) SHEET 1 AA1 4 PHE A 22 ILE A 25 0 SHEET 2 AA1 4 LYS A 104 ILE A 112 -1 O LYS A 104 N ILE A 25 SHEET 3 AA1 4 LYS A 42 VAL A 49 -1 N GLY A 44 O ASP A 111 SHEET 4 AA1 4 SER A 77 ALA A 83 -1 O PHE A 82 N MET A 43 SHEET 1 AA2 4 ALA A 29 VAL A 37 0 SHEET 2 AA2 4 GLY A 88 ASN A 96 -1 O TYR A 90 N GLU A 35 SHEET 3 AA2 4 ILE A 57 THR A 62 -1 N GLU A 60 O CYS A 93 SHEET 4 AA2 4 GLY A 68 GLU A 75 -1 O GLY A 72 N VAL A 59 SHEET 1 AA3 4 PHE B 22 ILE B 25 0 SHEET 2 AA3 4 LYS B 104 ILE B 112 -1 O LYS B 104 N ILE B 25 SHEET 3 AA3 4 LYS B 42 GLU B 51 -1 N GLY B 44 O ASP B 111 SHEET 4 AA3 4 SER B 77 ALA B 83 -1 O PHE B 82 N MET B 43 SHEET 1 AA4 4 ALA B 29 VAL B 37 0 SHEET 2 AA4 4 GLY B 88 ASN B 96 -1 O PHE B 92 N PHE B 33 SHEET 3 AA4 4 ILE B 57 THR B 62 -1 N GLU B 60 O CYS B 93 SHEET 4 AA4 4 GLY B 68 GLU B 75 -1 O ILE B 69 N ILE B 61 SSBOND 1 CYS A 32 CYS A 93 1555 1555 2.07 SSBOND 2 CYS B 32 CYS B 93 1555 1555 2.08 SITE 1 AC1 3 GLY A 20 TYR A 21 MET A 107 SITE 1 AC2 7 HOH A 312 ARG B 36 PRO B 64 MET B 86 SITE 2 AC2 7 GLY B 88 THR B 89 HOH B 309 CRYST1 97.772 35.664 62.312 90.00 129.22 90.00 C 1 2 1 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 0.010228 0.000000 0.008348 0.00000 SCALE2 0.000000 0.028039 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020715 0.00000