HEADER PROTEIN TRANSPORT 18-SEP-12 4H5I TITLE CRYSTAL STRUCTURE OF THE GUANINE NUCLEOTIDE EXCHANGE FACTOR SEC12 (P1 TITLE 2 FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANINE NUCLEOTIDE-EXCHANGE FACTOR SEC12; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-354; COMPND 5 SYNONYM: PROTEIN TRANSPORT PROTEIN SEC12; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: SEC12, SED2, YNR026C, N3244; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS COPII VESICLE BUDDING, POTASSIUM BINDING SITE, BETA PROPELLER, KEYWDS 2 PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.MCMAHON,P.D.JEFFREY,F.M.HUGHSON REVDAT 3 09-JAN-13 4H5I 1 JRNL REVDAT 2 14-NOV-12 4H5I 1 JRNL REVDAT 1 07-NOV-12 4H5I 0 JRNL AUTH C.MCMAHON,S.M.STUDER,C.CLENDINEN,G.P.DANN,P.D.JEFFREY, JRNL AUTH 2 F.M.HUGHSON JRNL TITL THE STRUCTURE OF SEC12 IMPLICATES POTASSIUM ION COORDINATION JRNL TITL 2 IN SAR1 ACTIVATION. JRNL REF J.BIOL.CHEM. V. 287 43599 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 23109340 JRNL DOI 10.1074/JBC.M112.420141 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1144) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 132033 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 6617 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 42.3800 - 4.2245 0.98 4353 234 0.1621 0.1649 REMARK 3 2 4.2245 - 3.3536 0.97 4244 226 0.1651 0.1795 REMARK 3 3 3.3536 - 2.9298 0.98 4362 216 0.1744 0.1879 REMARK 3 4 2.9298 - 2.6619 0.98 4293 222 0.1899 0.2187 REMARK 3 5 2.6619 - 2.4712 0.97 4336 243 0.1942 0.2019 REMARK 3 6 2.4712 - 2.3255 0.97 4280 238 0.1870 0.2041 REMARK 3 7 2.3255 - 2.2090 0.97 4257 236 0.1826 0.1957 REMARK 3 8 2.2090 - 2.1129 0.97 4312 208 0.1665 0.1798 REMARK 3 9 2.1129 - 2.0315 0.96 4249 200 0.1694 0.1950 REMARK 3 10 2.0315 - 1.9614 0.96 4299 211 0.1669 0.1789 REMARK 3 11 1.9614 - 1.9001 0.96 4215 229 0.1702 0.2039 REMARK 3 12 1.9001 - 1.8458 0.96 4246 201 0.1752 0.1901 REMARK 3 13 1.8458 - 1.7972 0.95 4231 246 0.1722 0.2100 REMARK 3 14 1.7972 - 1.7534 0.95 4219 209 0.1727 0.1837 REMARK 3 15 1.7534 - 1.7135 0.95 4184 227 0.1732 0.2047 REMARK 3 16 1.7135 - 1.6770 0.95 4152 225 0.1744 0.2086 REMARK 3 17 1.6770 - 1.6435 0.94 4187 233 0.1739 0.2013 REMARK 3 18 1.6435 - 1.6125 0.94 4153 221 0.1750 0.2022 REMARK 3 19 1.6125 - 1.5837 0.94 4200 215 0.1827 0.2159 REMARK 3 20 1.5837 - 1.5568 0.94 4138 230 0.1821 0.2137 REMARK 3 21 1.5568 - 1.5317 0.94 4159 212 0.1841 0.2243 REMARK 3 22 1.5317 - 1.5081 0.93 4091 204 0.1965 0.2038 REMARK 3 23 1.5081 - 1.4860 0.93 4067 225 0.1971 0.2234 REMARK 3 24 1.4860 - 1.4650 0.93 4125 234 0.2089 0.2475 REMARK 3 25 1.4650 - 1.4452 0.93 4059 231 0.2117 0.2157 REMARK 3 26 1.4452 - 1.4265 0.92 4118 211 0.2112 0.2456 REMARK 3 27 1.4265 - 1.4086 0.93 4045 216 0.2212 0.2439 REMARK 3 28 1.4086 - 1.3917 0.91 4110 210 0.2276 0.2641 REMARK 3 29 1.3917 - 1.3755 0.92 4046 226 0.2476 0.2564 REMARK 3 30 1.3755 - 1.3600 0.82 3686 178 0.2534 0.2887 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.02 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 : 0.011 5341 REMARK 3 ANGLE : 1.248 7223 REMARK 3 CHIRALITY : 0.088 865 REMARK 3 PLANARITY : 0.005 911 REMARK 3 DIHEDRAL : 12.132 1953 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 4H5I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-12. REMARK 100 THE RCSB ID CODE IS RCSB075044. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE CRYSTAL REMARK 200 SAGITTAL FOCUSING REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 132685 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 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 (%) : 93.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, PH 8.0, 400 MM POTASSIUM REMARK 280 CHLORIDE, 22% W/V PEG3350, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 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 MSE A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 TYR A 345 REMARK 465 THR A 346 REMARK 465 SER A 347 REMARK 465 MSE A 348 REMARK 465 LYS A 349 REMARK 465 GLN A 350 REMARK 465 LYS A 351 REMARK 465 ILE A 352 REMARK 465 SER A 353 REMARK 465 LYS A 354 REMARK 465 LEU A 355 REMARK 465 GLU A 356 REMARK 465 HIS A 357 REMARK 465 HIS A 358 REMARK 465 HIS A 359 REMARK 465 HIS A 360 REMARK 465 HIS A 361 REMARK 465 HIS A 362 REMARK 465 MSE B -2 REMARK 465 ALA B -1 REMARK 465 TYR B 345 REMARK 465 THR B 346 REMARK 465 SER B 347 REMARK 465 MSE B 348 REMARK 465 LYS B 349 REMARK 465 GLN B 350 REMARK 465 LYS B 351 REMARK 465 ILE B 352 REMARK 465 SER B 353 REMARK 465 LYS B 354 REMARK 465 LEU B 355 REMARK 465 GLU B 356 REMARK 465 HIS B 357 REMARK 465 HIS B 358 REMARK 465 HIS B 359 REMARK 465 HIS B 360 REMARK 465 HIS B 361 REMARK 465 HIS B 362 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER B 0 OG 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 B 663 O HOH B 666 2.08 REMARK 500 ND2 ASN B 253 O HOH B 682 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 714 O HOH B 570 1455 2.02 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 ASN A 21 -166.10 -166.08 REMARK 500 ASP A 212 45.43 -102.31 REMARK 500 ASN A 288 27.85 80.70 REMARK 500 ASN A 331 11.55 84.23 REMARK 500 ALA A 343 1.26 -65.40 REMARK 500 ASN B 21 -163.53 -160.25 REMARK 500 ASP B 212 47.60 -104.93 REMARK 500 ASN B 288 31.82 78.74 REMARK 500 ASN B 331 -1.96 94.34 REMARK 500 ALA B 343 0.39 -69.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 401 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 32 O REMARK 620 2 ILE B 38 O 108.2 REMARK 620 3 GLY B 34 O 92.4 141.9 REMARK 620 4 HOH B 501 O 161.7 88.2 78.5 REMARK 620 5 ASP B 68 O 70.4 122.8 93.9 94.2 REMARK 620 6 ASN B 36 OD1 113.0 72.8 69.7 78.9 163.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE B 222 O REMARK 620 2 LEU B 179 O 92.2 REMARK 620 3 TYR B 137 OH 158.2 92.9 REMARK 620 4 HOH B 530 O 82.5 151.0 82.8 REMARK 620 5 ASP B 178 OD1 71.7 96.2 86.6 55.1 REMARK 620 6 HOH B 626 O 115.7 140.8 71.7 64.6 117.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 402 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 222 O REMARK 620 2 LEU A 179 O 92.5 REMARK 620 3 TYR A 137 OH 157.5 92.1 REMARK 620 4 HOH A 516 O 81.6 151.1 83.8 REMARK 620 5 ASP A 178 OD1 71.3 95.9 86.3 55.3 REMARK 620 6 HOH A 622 O 116.4 136.7 73.5 69.3 122.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 401 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 32 O REMARK 620 2 GLY A 34 O 92.5 REMARK 620 3 ASP A 68 O 73.2 94.0 REMARK 620 4 ASN A 36 OD1 112.0 71.8 164.8 REMARK 620 5 HOH A 501 O 158.5 73.7 91.1 79.7 REMARK 620 6 ILE A 38 O 106.4 144.3 120.1 73.1 94.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4H5J RELATED DB: PDB REMARK 900 SEC12 IN AN ALTERNATE P64 CRYSTAL FORM DBREF 4H5I A 1 354 UNP P11655 SEC12_YEAST 1 354 DBREF 4H5I B 1 354 UNP P11655 SEC12_YEAST 1 354 SEQADV 4H5I MSE A -2 UNP P11655 EXPRESSION TAG SEQADV 4H5I ALA A -1 UNP P11655 EXPRESSION TAG SEQADV 4H5I SER A 0 UNP P11655 EXPRESSION TAG SEQADV 4H5I LEU A 355 UNP P11655 EXPRESSION TAG SEQADV 4H5I GLU A 356 UNP P11655 EXPRESSION TAG SEQADV 4H5I HIS A 357 UNP P11655 EXPRESSION TAG SEQADV 4H5I HIS A 358 UNP P11655 EXPRESSION TAG SEQADV 4H5I HIS A 359 UNP P11655 EXPRESSION TAG SEQADV 4H5I HIS A 360 UNP P11655 EXPRESSION TAG SEQADV 4H5I HIS A 361 UNP P11655 EXPRESSION TAG SEQADV 4H5I HIS A 362 UNP P11655 EXPRESSION TAG SEQADV 4H5I MSE B -2 UNP P11655 EXPRESSION TAG SEQADV 4H5I ALA B -1 UNP P11655 EXPRESSION TAG SEQADV 4H5I SER B 0 UNP P11655 EXPRESSION TAG SEQADV 4H5I LEU B 355 UNP P11655 EXPRESSION TAG SEQADV 4H5I GLU B 356 UNP P11655 EXPRESSION TAG SEQADV 4H5I HIS B 357 UNP P11655 EXPRESSION TAG SEQADV 4H5I HIS B 358 UNP P11655 EXPRESSION TAG SEQADV 4H5I HIS B 359 UNP P11655 EXPRESSION TAG SEQADV 4H5I HIS B 360 UNP P11655 EXPRESSION TAG SEQADV 4H5I HIS B 361 UNP P11655 EXPRESSION TAG SEQADV 4H5I HIS B 362 UNP P11655 EXPRESSION TAG SEQRES 1 A 365 MSE ALA SER MSE LYS PHE VAL THR ALA SER TYR ASN VAL SEQRES 2 A 365 GLY TYR PRO ALA TYR GLY ALA LYS PHE LEU ASN ASN ASP SEQRES 3 A 365 THR LEU LEU VAL ALA GLY GLY GLY GLY GLU GLY ASN ASN SEQRES 4 A 365 GLY ILE PRO ASN LYS LEU THR VAL LEU ARG VAL ASP PRO SEQRES 5 A 365 THR LYS ASP THR GLU LYS GLU GLN PHE HIS ILE LEU SER SEQRES 6 A 365 GLU PHE ALA LEU GLU ASP ASN ASP ASP SER PRO THR ALA SEQRES 7 A 365 ILE ASP ALA SER LYS GLY ILE ILE LEU VAL GLY CYS ASN SEQRES 8 A 365 GLU ASN SER THR LYS ILE THR GLN GLY LYS GLY ASN LYS SEQRES 9 A 365 HIS LEU ARG LYS PHE LYS TYR ASP LYS VAL ASN ASP GLN SEQRES 10 A 365 LEU GLU PHE LEU THR SER VAL ASP PHE ASP ALA SER THR SEQRES 11 A 365 ASN ALA ASP ASP TYR THR LYS LEU VAL TYR ILE SER ARG SEQRES 12 A 365 GLU GLY THR VAL ALA ALA ILE ALA SER SER LYS VAL PRO SEQRES 13 A 365 ALA ILE MSE ARG ILE ILE ASP PRO SER ASP LEU THR GLU SEQRES 14 A 365 LYS PHE GLU ILE GLU THR ARG GLY GLU VAL LYS ASP LEU SEQRES 15 A 365 HIS PHE SER THR ASP GLY LYS VAL VAL ALA TYR ILE THR SEQRES 16 A 365 GLY SER SER LEU GLU VAL ILE SER THR VAL THR GLY SER SEQRES 17 A 365 CYS ILE ALA ARG LYS THR ASP PHE ASP LYS ASN TRP SER SEQRES 18 A 365 LEU SER LYS ILE ASN PHE ILE ALA ASP ASP THR VAL LEU SEQRES 19 A 365 ILE ALA ALA SER LEU LYS LYS GLY LYS GLY ILE VAL LEU SEQRES 20 A 365 THR LYS ILE SER ILE LYS SER GLY ASN THR SER VAL LEU SEQRES 21 A 365 ARG SER LYS GLN VAL THR ASN ARG PHE LYS GLY ILE THR SEQRES 22 A 365 SER MSE ASP VAL ASP MSE LYS GLY GLU LEU ALA VAL LEU SEQRES 23 A 365 ALA SER ASN ASP ASN SER ILE ALA LEU VAL LYS LEU LYS SEQRES 24 A 365 ASP LEU SER MSE SER LYS ILE PHE LYS GLN ALA HIS SER SEQRES 25 A 365 PHE ALA ILE THR GLU VAL THR ILE SER PRO ASP SER THR SEQRES 26 A 365 TYR VAL ALA SER VAL SER ALA ALA ASN THR ILE HIS ILE SEQRES 27 A 365 ILE LYS LEU PRO LEU ASN TYR ALA ASN TYR THR SER MSE SEQRES 28 A 365 LYS GLN LYS ILE SER LYS LEU GLU HIS HIS HIS HIS HIS SEQRES 29 A 365 HIS SEQRES 1 B 365 MSE ALA SER MSE LYS PHE VAL THR ALA SER TYR ASN VAL SEQRES 2 B 365 GLY TYR PRO ALA TYR GLY ALA LYS PHE LEU ASN ASN ASP SEQRES 3 B 365 THR LEU LEU VAL ALA GLY GLY GLY GLY GLU GLY ASN ASN SEQRES 4 B 365 GLY ILE PRO ASN LYS LEU THR VAL LEU ARG VAL ASP PRO SEQRES 5 B 365 THR LYS ASP THR GLU LYS GLU GLN PHE HIS ILE LEU SER SEQRES 6 B 365 GLU PHE ALA LEU GLU ASP ASN ASP ASP SER PRO THR ALA SEQRES 7 B 365 ILE ASP ALA SER LYS GLY ILE ILE LEU VAL GLY CYS ASN SEQRES 8 B 365 GLU ASN SER THR LYS ILE THR GLN GLY LYS GLY ASN LYS SEQRES 9 B 365 HIS LEU ARG LYS PHE LYS TYR ASP LYS VAL ASN ASP GLN SEQRES 10 B 365 LEU GLU PHE LEU THR SER VAL ASP PHE ASP ALA SER THR SEQRES 11 B 365 ASN ALA ASP ASP TYR THR LYS LEU VAL TYR ILE SER ARG SEQRES 12 B 365 GLU GLY THR VAL ALA ALA ILE ALA SER SER LYS VAL PRO SEQRES 13 B 365 ALA ILE MSE ARG ILE ILE ASP PRO SER ASP LEU THR GLU SEQRES 14 B 365 LYS PHE GLU ILE GLU THR ARG GLY GLU VAL LYS ASP LEU SEQRES 15 B 365 HIS PHE SER THR ASP GLY LYS VAL VAL ALA TYR ILE THR SEQRES 16 B 365 GLY SER SER LEU GLU VAL ILE SER THR VAL THR GLY SER SEQRES 17 B 365 CYS ILE ALA ARG LYS THR ASP PHE ASP LYS ASN TRP SER SEQRES 18 B 365 LEU SER LYS ILE ASN PHE ILE ALA ASP ASP THR VAL LEU SEQRES 19 B 365 ILE ALA ALA SER LEU LYS LYS GLY LYS GLY ILE VAL LEU SEQRES 20 B 365 THR LYS ILE SER ILE LYS SER GLY ASN THR SER VAL LEU SEQRES 21 B 365 ARG SER LYS GLN VAL THR ASN ARG PHE LYS GLY ILE THR SEQRES 22 B 365 SER MSE ASP VAL ASP MSE LYS GLY GLU LEU ALA VAL LEU SEQRES 23 B 365 ALA SER ASN ASP ASN SER ILE ALA LEU VAL LYS LEU LYS SEQRES 24 B 365 ASP LEU SER MSE SER LYS ILE PHE LYS GLN ALA HIS SER SEQRES 25 B 365 PHE ALA ILE THR GLU VAL THR ILE SER PRO ASP SER THR SEQRES 26 B 365 TYR VAL ALA SER VAL SER ALA ALA ASN THR ILE HIS ILE SEQRES 27 B 365 ILE LYS LEU PRO LEU ASN TYR ALA ASN TYR THR SER MSE SEQRES 28 B 365 LYS GLN LYS ILE SER LYS LEU GLU HIS HIS HIS HIS HIS SEQRES 29 B 365 HIS MODRES 4H5I MSE A 1 MET SELENOMETHIONINE MODRES 4H5I MSE A 156 MET SELENOMETHIONINE MODRES 4H5I MSE A 272 MET SELENOMETHIONINE MODRES 4H5I MSE A 276 MET SELENOMETHIONINE MODRES 4H5I MSE A 300 MET SELENOMETHIONINE MODRES 4H5I MSE B 1 MET SELENOMETHIONINE MODRES 4H5I MSE B 156 MET SELENOMETHIONINE MODRES 4H5I MSE B 272 MET SELENOMETHIONINE MODRES 4H5I MSE B 276 MET SELENOMETHIONINE MODRES 4H5I MSE B 300 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 156 8 HET MSE A 272 8 HET MSE A 276 8 HET MSE A 300 8 HET MSE B 1 8 HET MSE B 156 8 HET MSE B 272 8 HET MSE B 276 8 HET MSE B 300 8 HET K A 401 1 HET K A 402 1 HET K B 401 1 HET K B 402 1 HETNAM MSE SELENOMETHIONINE HETNAM K POTASSIUM ION FORMUL 1 MSE 10(C5 H11 N O2 SE) FORMUL 3 K 4(K 1+) FORMUL 7 HOH *428(H2 O) HELIX 1 1 THR A 53 GLN A 57 1 5 HELIX 2 2 ASN A 90 GLY A 97 1 8 HELIX 3 3 THR B 53 GLN B 57 1 5 HELIX 4 4 ASN B 90 GLY B 97 1 8 SHEET 1 A 4 THR A 5 ASN A 9 0 SHEET 2 A 4 THR A 332 LYS A 337 -1 O ILE A 335 N ALA A 6 SHEET 3 A 4 TYR A 323 SER A 328 -1 N SER A 326 O HIS A 334 SHEET 4 A 4 ILE A 312 ILE A 317 -1 N THR A 316 O ALA A 325 SHEET 1 B 4 ALA A 14 ASN A 21 0 SHEET 2 B 4 THR A 24 GLY A 30 -1 O LEU A 26 N LYS A 18 SHEET 3 B 4 ASN A 40 VAL A 47 -1 O LEU A 45 N LEU A 25 SHEET 4 B 4 PHE A 58 ALA A 65 -1 O LEU A 61 N VAL A 44 SHEET 1 C 4 ALA A 75 SER A 79 0 SHEET 2 C 4 ILE A 82 GLY A 86 -1 O GLY A 86 N ALA A 75 SHEET 3 C 4 LEU A 103 ASP A 109 -1 O ARG A 104 N VAL A 85 SHEET 4 C 4 GLN A 114 VAL A 121 -1 O GLN A 114 N ASP A 109 SHEET 1 D 4 THR A 133 ILE A 138 0 SHEET 2 D 4 ALA A 145 SER A 149 -1 O ALA A 146 N TYR A 137 SHEET 3 D 4 ILE A 155 ASP A 160 -1 O ILE A 159 N ALA A 145 SHEET 4 D 4 THR A 165 GLU A 171 -1 O LYS A 167 N ILE A 158 SHEET 1 E 4 ASP A 178 PHE A 181 0 SHEET 2 E 4 VAL A 187 ILE A 191 -1 O ALA A 189 N HIS A 180 SHEET 3 E 4 LEU A 196 SER A 200 -1 O ILE A 199 N VAL A 188 SHEET 4 E 4 CYS A 206 LYS A 210 -1 O ILE A 207 N VAL A 198 SHEET 1 F 4 TRP A 217 ALA A 226 0 SHEET 2 F 4 THR A 229 LEU A 236 -1 O LEU A 231 N ASN A 223 SHEET 3 F 4 ILE A 242 LYS A 250 -1 O ILE A 247 N VAL A 230 SHEET 4 F 4 ASN A 253 THR A 263 -1 O ASN A 253 N LYS A 250 SHEET 1 G 4 ILE A 269 VAL A 274 0 SHEET 2 G 4 LEU A 280 SER A 285 -1 O VAL A 282 N ASP A 273 SHEET 3 G 4 ILE A 290 LYS A 294 -1 O VAL A 293 N ALA A 281 SHEET 4 G 4 SER A 299 PHE A 304 -1 O PHE A 304 N ILE A 290 SHEET 1 H 4 THR B 5 ASN B 9 0 SHEET 2 H 4 THR B 332 LYS B 337 -1 O ILE B 335 N ALA B 6 SHEET 3 H 4 TYR B 323 SER B 328 -1 N SER B 326 O HIS B 334 SHEET 4 H 4 ILE B 312 ILE B 317 -1 N THR B 316 O ALA B 325 SHEET 1 I 4 ALA B 14 ASN B 21 0 SHEET 2 I 4 THR B 24 GLY B 30 -1 O LEU B 26 N LYS B 18 SHEET 3 I 4 ASN B 40 VAL B 47 -1 O LEU B 45 N LEU B 25 SHEET 4 I 4 PHE B 58 ALA B 65 -1 O SER B 62 N VAL B 44 SHEET 1 J 4 ALA B 75 SER B 79 0 SHEET 2 J 4 ILE B 82 GLY B 86 -1 O GLY B 86 N ALA B 75 SHEET 3 J 4 LEU B 103 ASP B 109 -1 O ARG B 104 N VAL B 85 SHEET 4 J 4 GLN B 114 VAL B 121 -1 O GLN B 114 N ASP B 109 SHEET 1 K 4 THR B 133 ILE B 138 0 SHEET 2 K 4 ALA B 145 SER B 149 -1 O ALA B 146 N TYR B 137 SHEET 3 K 4 ILE B 155 ASP B 160 -1 O ARG B 157 N ILE B 147 SHEET 4 K 4 THR B 165 GLU B 171 -1 O LYS B 167 N ILE B 158 SHEET 1 L 4 ASP B 178 PHE B 181 0 SHEET 2 L 4 VAL B 187 ILE B 191 -1 O ALA B 189 N HIS B 180 SHEET 3 L 4 LEU B 196 SER B 200 -1 O ILE B 199 N VAL B 188 SHEET 4 L 4 CYS B 206 LYS B 210 -1 O ILE B 207 N VAL B 198 SHEET 1 M 4 TRP B 217 ALA B 226 0 SHEET 2 M 4 THR B 229 LEU B 236 -1 O LEU B 231 N ASN B 223 SHEET 3 M 4 ILE B 242 LYS B 250 -1 O VAL B 243 N ALA B 234 SHEET 4 M 4 ASN B 253 THR B 263 -1 O ASN B 253 N LYS B 250 SHEET 1 N 4 ILE B 269 VAL B 274 0 SHEET 2 N 4 LEU B 280 SER B 285 -1 O VAL B 282 N ASP B 273 SHEET 3 N 4 ILE B 290 LYS B 294 -1 O VAL B 293 N ALA B 281 SHEET 4 N 4 SER B 299 PHE B 304 -1 O PHE B 304 N ILE B 290 SSBOND 1 CYS A 206 CYS B 206 1555 1465 2.04 LINK C MSE A 1 N LYS A 2 1555 1555 1.33 LINK C ILE A 155 N MSE A 156 1555 1555 1.33 LINK C MSE A 156 N ARG A 157 1555 1555 1.33 LINK C SER A 271 N MSE A 272 1555 1555 1.33 LINK C MSE A 272 N ASP A 273 1555 1555 1.33 LINK C ASP A 275 N MSE A 276 1555 1555 1.33 LINK C MSE A 276 N LYS A 277 1555 1555 1.33 LINK C SER A 299 N MSE A 300 1555 1555 1.33 LINK C MSE A 300 N SER A 301 1555 1555 1.32 LINK C SER B 0 N MSE B 1 1555 1555 1.33 LINK C MSE B 1 N LYS B 2 1555 1555 1.33 LINK C ILE B 155 N MSE B 156 1555 1555 1.32 LINK C MSE B 156 N ARG B 157 1555 1555 1.33 LINK C SER B 271 N MSE B 272 1555 1555 1.33 LINK C MSE B 272 N ASP B 273 1555 1555 1.33 LINK C ASP B 275 N MSE B 276 1555 1555 1.33 LINK C MSE B 276 N LYS B 277 1555 1555 1.33 LINK C SER B 299 N MSE B 300 1555 1555 1.33 LINK C MSE B 300 N SER B 301 1555 1555 1.32 LINK O GLY B 32 K K B 401 1555 1555 2.63 LINK O ILE B 222 K K B 402 1555 1555 2.64 LINK O ILE A 222 K K A 402 1555 1555 2.64 LINK O GLY A 32 K K A 401 1555 1555 2.65 LINK O LEU B 179 K K B 402 1555 1555 2.74 LINK O LEU A 179 K K A 402 1555 1555 2.76 LINK O GLY A 34 K K A 401 1555 1555 2.77 LINK O ILE B 38 K K B 401 1555 1555 2.78 LINK OH TYR A 137 K K A 402 1555 1555 2.78 LINK O ASP A 68 K K A 401 1555 1555 2.79 LINK OD1 ASN A 36 K K A 401 1555 1555 2.80 LINK O GLY B 34 K K B 401 1555 1555 2.80 LINK OH TYR B 137 K K B 402 1555 1555 2.81 LINK O HOH A 501 K K A 401 1555 1555 2.86 LINK O HOH B 501 K K B 401 1555 1555 2.86 LINK O HOH B 530 K K B 402 1555 1555 2.88 LINK O HOH A 516 K K A 402 1555 1555 2.89 LINK O ASP B 68 K K B 401 1555 1555 2.91 LINK OD1 ASN B 36 K K B 401 1555 1555 2.91 LINK O ILE A 38 K K A 401 1555 1555 2.96 LINK OD1 ASP A 178 K K A 402 1555 1555 3.01 LINK OD1 ASP B 178 K K B 402 1555 1555 3.02 LINK O HOH B 626 K K B 402 1555 1555 3.25 LINK O HOH A 622 K K A 402 1555 1555 3.27 CISPEP 1 VAL A 152 PRO A 153 0 2.61 CISPEP 2 VAL B 152 PRO B 153 0 -0.39 SITE 1 AC1 6 GLY A 32 GLY A 34 ASN A 36 ILE A 38 SITE 2 AC1 6 ASP A 68 HOH A 501 SITE 1 AC2 6 TYR A 137 ASP A 178 LEU A 179 HIS A 180 SITE 2 AC2 6 ILE A 222 HOH A 516 SITE 1 AC3 6 GLY B 32 GLY B 34 ASN B 36 ILE B 38 SITE 2 AC3 6 ASP B 68 HOH B 501 SITE 1 AC4 7 TYR B 137 ASP B 178 LEU B 179 HIS B 180 SITE 2 AC4 7 ILE B 222 ASN B 223 HOH B 530 CRYST1 53.400 53.474 61.976 81.68 73.37 87.58 P 1 2 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 0.018727 -0.000790 -0.005539 0.00000 SCALE2 0.000000 0.018717 -0.002617 0.00000 SCALE3 0.000000 0.000000 0.017004 0.00000 HETATM 1 N MSE A 1 47.647 14.124 1.309 1.00 38.14 N HETATM 2 CA MSE A 1 47.361 13.153 2.363 1.00 41.07 C HETATM 3 C MSE A 1 46.446 12.021 1.910 1.00 37.60 C HETATM 4 O MSE A 1 45.365 12.258 1.366 1.00 31.22 O HETATM 5 CB MSE A 1 46.743 13.828 3.577 1.00 36.84 C HETATM 6 CG MSE A 1 46.053 12.837 4.478 1.00 36.41 C HETATM 7 SE MSE A 1 45.772 13.473 6.272 1.00 80.11 SE HETATM 8 CE MSE A 1 44.866 11.923 6.941 1.00 30.05 C