HEADER METAL BINDING PROTEIN 26-APR-12 4EVF TITLE CRYSTAL STRUCTURE OF APO ALPHA-1 GIARDIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GIARDIN SUBUNIT ALPHA-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALPHA-1 GIARDIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GIARDIA INTESTINALIS; SOURCE 3 ORGANISM_COMMON: GIARDIA LAMBLIA; SOURCE 4 ORGANISM_TAXID: 5741; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRSET_6C KEYWDS ANNEXIN, CALCIUM-BINDING PROTEIN, MEMBRANE-BINDING PROTEIN, METAL KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.WEERATUNGA,A.HOFMANN REVDAT 3 20-MAR-24 4EVF 1 REMARK REVDAT 2 17-JUL-13 4EVF 1 JRNL REVDAT 1 25-JUL-12 4EVF 0 JRNL AUTH S.K.WEERATUNGA,A.OSMAN,N.-J.HU,C.K.WANG,L.MASON,S.SVARD, JRNL AUTH 2 G.HOPE,M.K.JONES,A.HOFMANN JRNL TITL ALPHA-1 GIARDIN IS AN ANNEXIN WITH HIGHLY UNUSUAL JRNL TITL 2 CALCIUM-REGULATED MECHANISMS JRNL REF J.MOL.BIOL. V. 423 169 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22796298 JRNL DOI 10.1016/J.JMB.2012.06.041 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 44056 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 2252 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 24.8282 - 4.7770 0.92 2521 117 0.1891 0.2501 REMARK 3 2 4.7770 - 3.7960 0.98 2678 138 0.1465 0.1909 REMARK 3 3 3.7960 - 3.3175 0.99 2684 150 0.1752 0.2232 REMARK 3 4 3.3175 - 3.0147 1.00 2677 154 0.1893 0.2605 REMARK 3 5 3.0147 - 2.7990 0.99 2714 123 0.1971 0.2661 REMARK 3 6 2.7990 - 2.6341 0.99 2729 136 0.2096 0.2584 REMARK 3 7 2.6341 - 2.5023 0.98 2634 170 0.2080 0.3220 REMARK 3 8 2.5023 - 2.3935 0.97 2665 133 0.2395 0.2882 REMARK 3 9 2.3935 - 2.3014 0.96 2583 167 0.2226 0.3112 REMARK 3 10 2.3014 - 2.2221 0.97 2602 149 0.2289 0.3268 REMARK 3 11 2.2221 - 2.1526 0.95 2615 126 0.2270 0.2700 REMARK 3 12 2.1526 - 2.0911 0.94 2592 136 0.2292 0.2632 REMARK 3 13 2.0911 - 2.0361 0.95 2518 129 0.2274 0.2861 REMARK 3 14 2.0361 - 1.9864 0.93 2559 154 0.2512 0.3211 REMARK 3 15 1.9864 - 1.9413 0.93 2537 121 0.2739 0.3728 REMARK 3 16 1.9413 - 1.9000 0.93 2496 149 0.3020 0.3815 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 46.11 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.00120 REMARK 3 B22 (A**2) : -7.64980 REMARK 3 B33 (A**2) : 0.64850 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 2417 REMARK 3 ANGLE : 0.972 3251 REMARK 3 CHIRALITY : 0.070 344 REMARK 3 PLANARITY : 0.004 419 REMARK 3 DIHEDRAL : 15.221 913 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: THE FRIEDEL PAIRS WERE USED FOR REMARK 3 PHASING. REMARK 4 REMARK 4 4EVF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072117. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-06; 11-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SRS; AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : PX10.1; MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488; 1.25474, 1.25418, 1.37756 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; ADSC QUANTUM REMARK 200 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47848 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 1.0 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12300 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38200 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE STRUCTURAL FACTOR FILE CONTAINS FRIEDEL PAIRS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MGCL2, 30% PEG 2000, 20MM KH2PO4, REMARK 280 PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 25.63350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.85000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.37350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.85000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.63350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.37350 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 MET A 1 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 59 CG CD CE NZ REMARK 480 LYS A 120 CD CE NZ REMARK 480 LYS A 169 CD CE NZ REMARK 480 LYS A 267 CD CE NZ 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 NZ LYS A 295 O HOH A 510 1.97 REMARK 500 NH1 ARG A 35 O HOH A 371 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 LYS A 211 -135.73 57.52 REMARK 500 ASP A 241 41.15 -85.10 REMARK 500 ASP A 244 97.43 -67.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EVH RELATED DB: PDB DBREF 4EVF A 1 295 UNP P17063 GIA1_GIAIN 1 295 SEQRES 1 A 295 MET PRO LYS VAL THR ASP ILE ALA ASN GLU LEU LYS GLN SEQRES 2 A 295 ALA ILE ASP ALA LYS ASP GLU VAL GLN ILE ALA PHE ILE SEQRES 3 A 295 ALA SER GLU TYR SER ALA GLU SER ARG GLU LYS ILE ALA SEQRES 4 A 295 LYS ALA TYR VAL ALA SER TYR GLY LYS GLU LEU PRO ASP SEQRES 5 A 295 ASP ILE LYS LYS ALA LEU LYS GLY GLY SER GLU GLU SER SEQRES 6 A 295 LEU LEU MET ASP LEU PHE SER ASP ARG HIS GLU VAL ARG SEQRES 7 A 295 ALA GLN HIS ILE ARG ASP ALA LEU SER GLY ARG ASN ASP SEQRES 8 A 295 HIS MET ALA PHE PHE ASP THR VAL ILE LEU CYS THR PRO SEQRES 9 A 295 GLU ASP TRP HIS GLU THR VAL ALA ALA TYR THR ARG MET SEQRES 10 A 295 PHE LYS LYS PRO LEU VAL GLU ASP PHE MET LYS ASP VAL SEQRES 11 A 295 GLY ARG LYS GLU ASP TRP CYS LEU LEU MET GLU LYS TRP SEQRES 12 A 295 MET ALA HIS GLU ARG VAL SER ARG PRO GLY SER PRO GLU SEQRES 13 A 295 ASP GLU ALA GLN ARG LEU ASP GLN ALA PHE ASP GLN LYS SEQRES 14 A 295 ASN THR ALA TYR LEU ILE ASP PHE PHE GLY THR VAL PRO SEQRES 15 A 295 SER ALA GLU TYR ARG PRO ILE ALA GLU ALA PHE LYS ALA SEQRES 16 A 295 GLN ASN GLY LYS SER ILE GLU GLN ALA ILE ALA THR ILE SEQRES 17 A 295 TYR THR LYS THR ASP TYR TYR THR PHE TYR CYS ALA HIS SEQRES 18 A 295 PHE ALA LEU LEU GLY MET HIS ARG LEU ALA ALA TYR LEU SEQRES 19 A 295 ILE ASN CYS ALA CYS ASN ASP LYS GLY ASP GLU LYS ARG SEQRES 20 A 295 MET ARG ARG ILE THR GLY MET MET VAL ASP LYS CYS LEU SEQRES 21 A 295 GLY ALA LYS HIS ALA TYR LYS ILE TYR GLY ASP MET GLY SEQRES 22 A 295 THR ASP ILE GLU ARG CYS PHE ASP LYS ARG MET ALA PRO SEQRES 23 A 295 ILE LEU ARG THR LEU TRP ARG VAL LYS FORMUL 2 HOH *286(H2 O) HELIX 1 1 LYS A 3 ALA A 17 1 15 HELIX 2 2 ASP A 19 GLU A 29 1 11 HELIX 3 3 SER A 31 GLY A 47 1 17 HELIX 4 4 GLU A 49 LEU A 58 1 10 HELIX 5 5 GLY A 61 PHE A 71 1 11 HELIX 6 6 ASP A 73 GLY A 88 1 16 HELIX 7 7 ASP A 91 ILE A 100 1 10 HELIX 8 8 THR A 103 LYS A 119 1 17 HELIX 9 9 PRO A 121 GLY A 131 1 11 HELIX 10 10 GLU A 134 HIS A 146 1 13 HELIX 11 11 SER A 154 GLN A 168 1 15 HELIX 12 12 ASN A 170 VAL A 181 1 12 HELIX 13 13 PRO A 182 ASN A 197 1 16 HELIX 14 14 SER A 200 TYR A 209 1 10 HELIX 15 15 THR A 210 GLY A 226 1 17 HELIX 16 16 GLY A 226 ASP A 241 1 16 HELIX 17 17 ASP A 244 VAL A 256 1 13 HELIX 18 18 ASP A 257 LEU A 260 5 4 HELIX 19 19 GLY A 261 TYR A 266 1 6 HELIX 20 20 LYS A 267 TYR A 269 5 3 HELIX 21 21 ASP A 271 PHE A 280 1 10 HELIX 22 22 ARG A 283 ARG A 293 1 11 CRYST1 51.267 58.747 99.700 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 0.019506 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010030 0.00000