HEADER TRANSPORT PROTEIN 04-FEB-19 6JE7 TITLE CRYSTAL STRUCTURE OF HUMAN SERUM ALBUMIN CRYSTALLIZED BY AMMONIUM TITLE 2 SULFATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERUM ALBUMIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS CARRIER PROTEIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.KITAHARA,S.FUDO,T.YONEDA,M.NUKAGA,T.HOSHINO REVDAT 3 22-NOV-23 6JE7 1 REMARK REVDAT 2 20-NOV-19 6JE7 1 JRNL REVDAT 1 27-MAR-19 6JE7 0 JRNL AUTH M.KITAHARA,S.FUDO,T.YONEDA,M.NUKAGA,T.HOSHINO JRNL TITL ANISOTROPIC DISTRIBUTION OF AMMONIUM SULFATE IONS IN PROTEIN JRNL TITL 2 CRYSTALLIZATION JRNL REF CRYST.GROWTH DES. V. 19 6004 2019 JRNL REFN ESSN 1528-7505 JRNL DOI 10.1021/ACS.CGD.9B00256 REMARK 2 REMARK 2 RESOLUTION. 3.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.6 REMARK 3 NUMBER OF REFLECTIONS : 6213 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.292 REMARK 3 R VALUE (WORKING SET) : 0.290 REMARK 3 FREE R VALUE : 0.326 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 305 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 29.0652 - 4.9098 0.95 3215 168 0.2820 0.3234 REMARK 3 2 4.9098 - 3.9000 0.81 2693 137 0.3056 0.3308 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.590 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 116.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 138.2 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 : 0.002 4742 REMARK 3 ANGLE : 0.468 6407 REMARK 3 CHIRALITY : 0.034 708 REMARK 3 PLANARITY : 0.003 830 REMARK 3 DIHEDRAL : 22.665 2985 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 6JE7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1300010961. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32372 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.9 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0460 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1AO6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M AMMONIUM SULFATE, 1%(V/V) 1,4 REMARK 280 -1,1,1,3,3,3-HEXAFLUORO-2-PROPANOL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 281K 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 83.48450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.51200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 83.48450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.51200 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 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 3 106.46 62.69 REMARK 500 ASN A 109 76.69 -117.63 REMARK 500 ASN A 130 84.16 -158.10 REMARK 500 ILE A 271 -68.55 -127.94 REMARK 500 ASP A 301 72.45 58.50 REMARK 500 VAL A 310 -46.01 -132.45 REMARK 500 ALA A 364 -75.81 -71.82 REMARK 500 LYS A 466 -7.10 66.54 REMARK 500 PHE A 507 67.16 -106.35 REMARK 500 CYS A 558 -33.97 -131.09 REMARK 500 LYS A 560 69.65 -107.64 REMARK 500 ALA A 561 66.20 -154.33 REMARK 500 ASP A 562 -165.15 58.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 6JE7 A 2 584 UNP P02768 ALBU_HUMAN 26 608 SEQRES 1 A 583 ALA HIS LYS SER GLU VAL ALA HIS ARG PHE LYS ASP LEU SEQRES 2 A 583 GLY GLU GLU ASN PHE LYS ALA LEU VAL LEU ILE ALA PHE SEQRES 3 A 583 ALA GLN TYR LEU GLN GLN CYS PRO PHE GLU ASP HIS VAL SEQRES 4 A 583 LYS LEU VAL ASN GLU VAL THR GLU PHE ALA LYS THR CYS SEQRES 5 A 583 VAL ALA ASP GLU SER ALA GLU ASN CYS ASP LYS SER LEU SEQRES 6 A 583 HIS THR LEU PHE GLY ASP LYS LEU CYS THR VAL ALA THR SEQRES 7 A 583 LEU ARG GLU THR TYR GLY GLU MET ALA ASP CYS CYS ALA SEQRES 8 A 583 LYS GLN GLU PRO GLU ARG ASN GLU CYS PHE LEU GLN HIS SEQRES 9 A 583 LYS ASP ASP ASN PRO ASN LEU PRO ARG LEU VAL ARG PRO SEQRES 10 A 583 GLU VAL ASP VAL MET CYS THR ALA PHE HIS ASP ASN GLU SEQRES 11 A 583 GLU THR PHE LEU LYS LYS TYR LEU TYR GLU ILE ALA ARG SEQRES 12 A 583 ARG HIS PRO TYR PHE TYR ALA PRO GLU LEU LEU PHE PHE SEQRES 13 A 583 ALA LYS ARG TYR LYS ALA ALA PHE THR GLU CYS CYS GLN SEQRES 14 A 583 ALA ALA ASP LYS ALA ALA CYS LEU LEU PRO LYS LEU ASP SEQRES 15 A 583 GLU LEU ARG ASP GLU GLY LYS ALA SER SER ALA LYS GLN SEQRES 16 A 583 ARG LEU LYS CYS ALA SER LEU GLN LYS PHE GLY GLU ARG SEQRES 17 A 583 ALA PHE LYS ALA TRP ALA VAL ALA ARG LEU SER GLN ARG SEQRES 18 A 583 PHE PRO LYS ALA GLU PHE ALA GLU VAL SER LYS LEU VAL SEQRES 19 A 583 THR ASP LEU THR LYS VAL HIS THR GLU CYS CYS HIS GLY SEQRES 20 A 583 ASP LEU LEU GLU CYS ALA ASP ASP ARG ALA ASP LEU ALA SEQRES 21 A 583 LYS TYR ILE CYS GLU ASN GLN ASP SER ILE SER SER LYS SEQRES 22 A 583 LEU LYS GLU CYS CYS GLU LYS PRO LEU LEU GLU LYS SER SEQRES 23 A 583 HIS CYS ILE ALA GLU VAL GLU ASN ASP GLU MET PRO ALA SEQRES 24 A 583 ASP LEU PRO SER LEU ALA ALA ASP PHE VAL GLU SER LYS SEQRES 25 A 583 ASP VAL CYS LYS ASN TYR ALA GLU ALA LYS ASP VAL PHE SEQRES 26 A 583 LEU GLY MET PHE LEU TYR GLU TYR ALA ARG ARG HIS PRO SEQRES 27 A 583 ASP TYR SER VAL VAL LEU LEU LEU ARG LEU ALA LYS THR SEQRES 28 A 583 TYR GLU THR THR LEU GLU LYS CYS CYS ALA ALA ALA ASP SEQRES 29 A 583 PRO HIS GLU CYS TYR ALA LYS VAL PHE ASP GLU PHE LYS SEQRES 30 A 583 PRO LEU VAL GLU GLU PRO GLN ASN LEU ILE LYS GLN ASN SEQRES 31 A 583 CYS GLU LEU PHE GLU GLN LEU GLY GLU TYR LYS PHE GLN SEQRES 32 A 583 ASN ALA LEU LEU VAL ARG TYR THR LYS LYS VAL PRO GLN SEQRES 33 A 583 VAL SER THR PRO THR LEU VAL GLU VAL SER ARG ASN LEU SEQRES 34 A 583 GLY LYS VAL GLY SER LYS CYS CYS LYS HIS PRO GLU ALA SEQRES 35 A 583 LYS ARG MET PRO CYS ALA GLU ASP TYR LEU SER VAL VAL SEQRES 36 A 583 LEU ASN GLN LEU CYS VAL LEU HIS GLU LYS THR PRO VAL SEQRES 37 A 583 SER ASP ARG VAL THR LYS CYS CYS THR GLU SER LEU VAL SEQRES 38 A 583 ASN ARG ARG PRO CYS PHE SER ALA LEU GLU VAL ASP GLU SEQRES 39 A 583 THR TYR VAL PRO LYS GLU PHE ASN ALA GLU THR PHE THR SEQRES 40 A 583 PHE HIS ALA ASP ILE CYS THR LEU SER GLU LYS GLU ARG SEQRES 41 A 583 GLN ILE LYS LYS GLN THR ALA LEU VAL GLU LEU VAL LYS SEQRES 42 A 583 HIS LYS PRO LYS ALA THR LYS GLU GLN LEU LYS ALA VAL SEQRES 43 A 583 MET ASP ASP PHE ALA ALA PHE VAL GLU LYS CYS CYS LYS SEQRES 44 A 583 ALA ASP ASP LYS GLU THR CYS PHE ALA GLU GLU GLY LYS SEQRES 45 A 583 LYS LEU VAL ALA ALA SER GLN ALA ALA LEU GLY HELIX 1 AA1 SER A 5 GLY A 15 1 11 HELIX 2 AA2 GLY A 15 LEU A 31 1 17 HELIX 3 AA3 PRO A 35 ASP A 56 1 22 HELIX 4 AA4 SER A 65 THR A 76 1 12 HELIX 5 AA5 THR A 79 TYR A 84 1 6 HELIX 6 AA6 GLY A 85 LYS A 93 5 9 HELIX 7 AA7 GLN A 94 HIS A 105 1 12 HELIX 8 AA8 GLU A 119 ASN A 130 1 12 HELIX 9 AA9 ASN A 130 HIS A 146 1 17 HELIX 10 AB1 TYR A 150 CYS A 169 1 20 HELIX 11 AB2 ASP A 173 GLY A 207 1 35 HELIX 12 AB3 GLY A 207 PHE A 223 1 17 HELIX 13 AB4 GLU A 227 GLY A 248 1 22 HELIX 14 AB5 ASP A 249 ASN A 267 1 19 HELIX 15 AB6 PRO A 282 VAL A 293 1 12 HELIX 16 AB7 LEU A 305 VAL A 310 1 6 HELIX 17 AB8 ASP A 314 ALA A 322 1 9 HELIX 18 AB9 ALA A 322 ARG A 337 1 16 HELIX 19 AC1 SER A 342 CYS A 361 1 20 HELIX 20 AC2 ASP A 365 TYR A 370 1 6 HELIX 21 AC3 ALA A 371 ASP A 375 5 5 HELIX 22 AC4 GLU A 376 GLN A 397 1 22 HELIX 23 AC5 GLY A 399 VAL A 415 1 17 HELIX 24 AC6 SER A 419 CYS A 437 1 19 HELIX 25 AC7 PRO A 441 ALA A 443 5 3 HELIX 26 AC8 LYS A 444 GLU A 465 1 22 HELIX 27 AC9 SER A 470 GLU A 479 1 10 HELIX 28 AD1 SER A 480 ALA A 490 1 11 HELIX 29 AD2 HIS A 510 THR A 515 5 6 HELIX 30 AD3 SER A 517 LYS A 536 1 20 HELIX 31 AD4 THR A 540 LYS A 560 1 21 HELIX 32 AD5 ALA A 569 LEU A 583 1 15 SSBOND 1 CYS A 53 CYS A 62 1555 1555 2.03 SSBOND 2 CYS A 75 CYS A 91 1555 1555 2.03 SSBOND 3 CYS A 90 CYS A 101 1555 1555 2.03 SSBOND 4 CYS A 124 CYS A 169 1555 1555 2.03 SSBOND 5 CYS A 168 CYS A 177 1555 1555 2.04 SSBOND 6 CYS A 200 CYS A 246 1555 1555 2.03 SSBOND 7 CYS A 245 CYS A 253 1555 1555 2.02 SSBOND 8 CYS A 265 CYS A 279 1555 1555 2.03 SSBOND 9 CYS A 278 CYS A 289 1555 1555 2.03 SSBOND 10 CYS A 316 CYS A 361 1555 1555 2.03 SSBOND 11 CYS A 360 CYS A 369 1555 1555 2.03 SSBOND 12 CYS A 392 CYS A 438 1555 1555 2.03 SSBOND 13 CYS A 437 CYS A 448 1555 1555 2.03 SSBOND 14 CYS A 461 CYS A 477 1555 1555 2.03 SSBOND 15 CYS A 476 CYS A 487 1555 1555 2.03 SSBOND 16 CYS A 514 CYS A 559 1555 1555 2.03 SSBOND 17 CYS A 558 CYS A 567 1555 1555 2.03 CRYST1 166.969 59.024 84.857 90.00 113.42 90.00 C 1 2 1 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 0.005989 0.000000 0.002594 0.00000 SCALE2 0.000000 0.016942 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012842 0.00000