HEADER TRANSFERASE 25-NOV-14 4X1T TITLE THE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA GALACTOLIPID SYNTHASE TITLE 2 MGD1 IN COMPLEX WITH UDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: MONOGALACTOSYLDIACYLGLYCEROL SYNTHASE 1, CHLOROPLASTIC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 137-533; COMPND 5 SYNONYM: ATMGD1,MGDG SYNTHASE TYPE A; COMPND 6 EC: 2.4.1.46; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: MGD1, MGDA, AT4G31780, F28M20.30; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MONOGALACTOSYLDIACYLGLYCEROL SYNTHASE, GT-B FOLD, KEYWDS 2 GLYCOSYLTRANSFERASE, GALACTOLIPID, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.ROCHA,C.BRETON REVDAT 4 10-JAN-24 4X1T 1 REMARK REVDAT 3 30-AUG-17 4X1T 1 REMARK SITE ATOM REVDAT 2 05-OCT-16 4X1T 1 JRNL REVDAT 1 10-FEB-16 4X1T 0 JRNL AUTH J.ROCHA,J.SARKIS,A.THOMAS,L.PITOU,J.RADZIMANOWSKI,M.AUDRY, JRNL AUTH 2 V.CHAZALET,D.DE SANCTIS,M.M.PALCIC,M.A.BLOCK,A.GIRARD-EGROT, JRNL AUTH 3 E.MARECHAL,C.BRETON JRNL TITL STRUCTURAL INSIGHTS AND MEMBRANE BINDING PROPERTIES OF MGD1, JRNL TITL 2 THE MAJOR GALACTOLIPID SYNTHASE IN PLANTS. JRNL REF PLANT J. V. 85 622 2016 JRNL REFN ESSN 1365-313X JRNL PMID 26935252 JRNL DOI 10.1111/TPJ.13129 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.280 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 20419 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1978 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 45.5896 - 5.4200 0.98 2617 129 0.2021 0.2102 REMARK 3 2 5.4200 - 4.3031 0.98 2636 120 0.1636 0.1951 REMARK 3 3 4.3031 - 3.7594 0.98 2609 128 0.1698 0.1369 REMARK 3 4 3.7594 - 3.4158 0.98 2623 148 0.1817 0.2376 REMARK 3 5 3.4158 - 3.1711 0.98 2559 153 0.2083 0.2195 REMARK 3 6 3.1711 - 2.9841 0.98 2643 149 0.2220 0.2711 REMARK 3 7 2.9841 - 2.8347 0.98 2583 149 0.2189 0.2581 REMARK 3 8 2.8347 - 2.7113 0.98 2646 119 0.2273 0.2686 REMARK 3 9 2.7113 - 2.6070 0.98 2657 120 0.2233 0.2364 REMARK 3 10 2.6070 - 2.5170 0.97 2579 153 0.2359 0.2538 REMARK 3 11 2.5170 - 2.4383 0.99 2590 173 0.2310 0.2512 REMARK 3 12 2.4383 - 2.3686 0.99 2590 151 0.2453 0.2813 REMARK 3 13 2.3686 - 2.3063 0.98 2669 152 0.2559 0.2354 REMARK 3 14 2.3063 - 2.2500 0.98 2567 134 0.2879 0.2699 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.970 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 2573 REMARK 3 ANGLE : 0.976 3458 REMARK 3 CHIRALITY : 0.047 393 REMARK 3 PLANARITY : 0.004 434 REMARK 3 DIHEDRAL : 16.632 983 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 142 THROUGH 324 ) REMARK 3 ORIGIN FOR THE GROUP (A): -36.4332 27.4447 10.3315 REMARK 3 T TENSOR REMARK 3 T11: 0.6428 T22: 0.4810 REMARK 3 T33: 1.2881 T12: -0.1160 REMARK 3 T13: 0.0752 T23: 0.1845 REMARK 3 L TENSOR REMARK 3 L11: 3.1145 L22: 3.0607 REMARK 3 L33: 2.7975 L12: 0.2525 REMARK 3 L13: 1.0114 L23: 0.2463 REMARK 3 S TENSOR REMARK 3 S11: 0.4234 S12: -0.2170 S13: -0.7082 REMARK 3 S21: 0.1531 S22: -0.1966 S23: -1.7614 REMARK 3 S31: 0.1662 S32: 0.4522 S33: -0.1709 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 325 THROUGH 474 ) REMARK 3 ORIGIN FOR THE GROUP (A): -62.2478 12.4122 6.3051 REMARK 3 T TENSOR REMARK 3 T11: 0.3892 T22: 0.1663 REMARK 3 T33: 0.1884 T12: 0.0252 REMARK 3 T13: 0.0761 T23: -0.0165 REMARK 3 L TENSOR REMARK 3 L11: 2.8117 L22: 5.9073 REMARK 3 L33: 2.7582 L12: 1.4675 REMARK 3 L13: 0.4157 L23: 0.7366 REMARK 3 S TENSOR REMARK 3 S11: 0.0108 S12: 0.2644 S13: -0.0650 REMARK 3 S21: -0.5524 S22: -0.0426 S23: -0.3885 REMARK 3 S31: -0.1146 S32: 0.2284 S33: 0.0445 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 475 THROUGH 525 ) REMARK 3 ORIGIN FOR THE GROUP (A): -56.5406 26.8748 6.6476 REMARK 3 T TENSOR REMARK 3 T11: 0.6739 T22: -0.0380 REMARK 3 T33: 0.4357 T12: 0.0117 REMARK 3 T13: 0.1834 T23: 0.0460 REMARK 3 L TENSOR REMARK 3 L11: 3.0206 L22: 2.8808 REMARK 3 L33: 1.8443 L12: 0.4958 REMARK 3 L13: -0.1334 L23: 0.6582 REMARK 3 S TENSOR REMARK 3 S11: 0.3830 S12: 0.5299 S13: 0.9285 REMARK 3 S21: -0.3388 S22: -0.0315 S23: -0.2209 REMARK 3 S31: -0.5883 S32: -0.0370 S33: -0.1553 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 4X1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000204551. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20423 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 45.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 20.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.53200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: 4WYI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-18% ETHYLENE GLYCOL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.13500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.13500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.13500 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 TOTAL BURIED SURFACE AREA: 2270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 13.0 KCAL/MOL 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 GLU A 137 REMARK 465 ALA A 138 REMARK 465 ASP A 139 REMARK 465 ARG A 140 REMARK 465 PRO A 141 REMARK 465 ASP A 180 REMARK 465 LEU A 181 REMARK 465 TRP A 182 REMARK 465 THR A 183 REMARK 465 ASP A 184 REMARK 465 HIS A 185 REMARK 465 THR A 186 REMARK 465 PRO A 187 REMARK 465 TRP A 188 REMARK 465 PRO A 189 REMARK 465 PHE A 190 REMARK 465 ASN A 191 REMARK 465 GLN A 192 REMARK 465 LEU A 193 REMARK 465 PRO A 194 REMARK 465 ARG A 195 REMARK 465 SER A 196 REMARK 465 TYR A 197 REMARK 465 ASN A 198 REMARK 465 PHE A 199 REMARK 465 LEU A 200 REMARK 465 VAL A 201 REMARK 465 LYS A 202 REMARK 465 HIS A 203 REMARK 465 GLY A 204 REMARK 465 THR A 205 REMARK 465 LEU A 206 REMARK 465 TRP A 207 REMARK 465 LYS A 208 REMARK 465 MET A 209 REMARK 465 THR A 210 REMARK 465 TYR A 211 REMARK 465 TYR A 212 REMARK 465 GLY A 213 REMARK 465 THR A 214 REMARK 465 SER A 215 REMARK 465 PRO A 216 REMARK 465 ARG A 217 REMARK 465 ILE A 218 REMARK 465 VAL A 219 REMARK 465 HIS A 220 REMARK 465 GLN A 221 REMARK 465 SER A 222 REMARK 465 ASN A 223 REMARK 465 PHE A 224 REMARK 465 ALA A 225 REMARK 465 ALA A 226 REMARK 465 THR A 227 REMARK 465 SER A 228 REMARK 465 THR A 229 REMARK 465 PHE A 230 REMARK 465 ILE A 231 REMARK 465 ALA A 232 REMARK 465 ARG A 233 REMARK 465 GLU A 234 REMARK 465 ILE A 235 REMARK 465 ALA A 236 REMARK 465 GLN A 237 REMARK 465 GLY A 238 REMARK 465 LEU A 239 REMARK 465 MET A 240 REMARK 465 LYS A 241 REMARK 465 TYR A 242 REMARK 465 LEU A 526 REMARK 465 PRO A 527 REMARK 465 GLN A 528 REMARK 465 LEU A 529 REMARK 465 SER A 530 REMARK 465 CYS A 531 REMARK 465 THR A 532 REMARK 465 ALA A 533 REMARK 465 ALA A 534 REMARK 465 ALA A 535 REMARK 465 ALA A 536 REMARK 465 LEU A 537 REMARK 465 GLU A 538 REMARK 465 HIS A 539 REMARK 465 HIS A 540 REMARK 465 HIS A 541 REMARK 465 HIS A 542 REMARK 465 HIS A 543 REMARK 465 HIS A 544 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 ASP A 150 N GLY A 152 2.11 REMARK 500 O PRO A 252 OG1 THR A 286 2.12 REMARK 500 OE1 GLU A 363 O HOH A 701 2.18 REMARK 500 O LYS A 290 NE2 GLN A 315 2.18 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 HG21 THR A 313 O2 EDO A 606 2565 1.45 REMARK 500 CG2 THR A 313 O2 EDO A 606 2565 2.00 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 VAL A 250 50.10 -115.70 REMARK 500 GLN A 255 -71.31 -114.11 REMARK 500 PRO A 285 -18.51 -41.87 REMARK 500 LYS A 416 59.09 -96.34 REMARK 500 GLU A 418 -58.77 -24.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 154 HIS A 155 31.11 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 UDP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 610 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WYI RELATED DB: PDB REMARK 900 4WYI CONTAINS THE SAME PROTEIN IN ITS APO-FORM DBREF 4X1T A 137 533 UNP O81770 MGDG1_ARATH 137 533 SEQADV 4X1T ALA A 534 UNP O81770 EXPRESSION TAG SEQADV 4X1T ALA A 535 UNP O81770 EXPRESSION TAG SEQADV 4X1T ALA A 536 UNP O81770 EXPRESSION TAG SEQADV 4X1T LEU A 537 UNP O81770 EXPRESSION TAG SEQADV 4X1T GLU A 538 UNP O81770 EXPRESSION TAG SEQADV 4X1T HIS A 539 UNP O81770 EXPRESSION TAG SEQADV 4X1T HIS A 540 UNP O81770 EXPRESSION TAG SEQADV 4X1T HIS A 541 UNP O81770 EXPRESSION TAG SEQADV 4X1T HIS A 542 UNP O81770 EXPRESSION TAG SEQADV 4X1T HIS A 543 UNP O81770 EXPRESSION TAG SEQADV 4X1T HIS A 544 UNP O81770 EXPRESSION TAG SEQRES 1 A 408 GLU ALA ASP ARG PRO LYS LYS VAL LEU ILE LEU MET SER SEQRES 2 A 408 ASP THR GLY GLY GLY HIS ARG ALA SER ALA GLU ALA ILE SEQRES 3 A 408 ARG ALA ALA PHE ASN GLN GLU PHE GLY ASP GLU TYR GLN SEQRES 4 A 408 VAL PHE ILE THR ASP LEU TRP THR ASP HIS THR PRO TRP SEQRES 5 A 408 PRO PHE ASN GLN LEU PRO ARG SER TYR ASN PHE LEU VAL SEQRES 6 A 408 LYS HIS GLY THR LEU TRP LYS MET THR TYR TYR GLY THR SEQRES 7 A 408 SER PRO ARG ILE VAL HIS GLN SER ASN PHE ALA ALA THR SEQRES 8 A 408 SER THR PHE ILE ALA ARG GLU ILE ALA GLN GLY LEU MET SEQRES 9 A 408 LYS TYR GLN PRO ASP ILE ILE ILE SER VAL HIS PRO LEU SEQRES 10 A 408 MET GLN HIS VAL PRO LEU ARG VAL LEU ARG SER LYS GLY SEQRES 11 A 408 LEU LEU LYS LYS ILE VAL PHE THR THR VAL ILE THR ASP SEQRES 12 A 408 LEU SER THR CYS HIS PRO THR TRP PHE HIS LYS LEU VAL SEQRES 13 A 408 THR ARG CYS TYR CYS PRO SER THR GLU VAL ALA LYS ARG SEQRES 14 A 408 ALA GLN LYS ALA GLY LEU GLU THR SER GLN ILE LYS VAL SEQRES 15 A 408 TYR GLY LEU PRO VAL ARG PRO SER PHE VAL LYS PRO VAL SEQRES 16 A 408 ARG PRO LYS VAL GLU LEU ARG ARG GLU LEU GLY MET ASP SEQRES 17 A 408 GLU ASN LEU PRO ALA VAL LEU LEU MET GLY GLY GLY GLU SEQRES 18 A 408 GLY MET GLY PRO ILE GLU ALA THR ALA ARG ALA LEU ALA SEQRES 19 A 408 ASP ALA LEU TYR ASP LYS ASN LEU GLY GLU ALA VAL GLY SEQRES 20 A 408 GLN VAL LEU ILE ILE CYS GLY ARG ASN LYS LYS LEU GLN SEQRES 21 A 408 SER LYS LEU SER SER LEU ASP TRP LYS ILE PRO VAL GLN SEQRES 22 A 408 VAL LYS GLY PHE ILE THR LYS MET GLU GLU CYS MET GLY SEQRES 23 A 408 ALA CYS ASP CYS ILE ILE THR LYS ALA GLY PRO GLY THR SEQRES 24 A 408 ILE ALA GLU ALA MET ILE ARG GLY LEU PRO ILE ILE LEU SEQRES 25 A 408 ASN GLY TYR ILE ALA GLY GLN GLU ALA GLY ASN VAL PRO SEQRES 26 A 408 TYR VAL VAL GLU ASN GLY CYS GLY LYS PHE SER LYS SER SEQRES 27 A 408 PRO LYS GLU ILE SER LYS ILE VAL ALA ASP TRP PHE GLY SEQRES 28 A 408 PRO ALA SER LYS GLU LEU GLU ILE MET SER GLN ASN ALA SEQRES 29 A 408 LEU ARG LEU ALA LYS PRO GLU ALA VAL PHE LYS ILE VAL SEQRES 30 A 408 HIS ASP MET HIS GLU LEU VAL ARG LYS LYS ASN SER LEU SEQRES 31 A 408 PRO GLN LEU SER CYS THR ALA ALA ALA ALA LEU GLU HIS SEQRES 32 A 408 HIS HIS HIS HIS HIS HET UDP A 601 36 HET EDO A 602 10 HET EDO A 603 10 HET EDO A 604 10 HET EDO A 605 10 HET EDO A 606 10 HET EDO A 607 10 HET EDO A 608 10 HET EDO A 609 10 HET EDO A 610 10 HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 UDP C9 H14 N2 O12 P2 FORMUL 3 EDO 9(C2 H6 O2) FORMUL 12 HOH *57(H2 O) HELIX 1 AA1 HIS A 155 GLY A 171 1 17 HELIX 2 AA2 ASP A 172 TYR A 174 5 3 HELIX 3 AA3 GLN A 255 SER A 264 1 10 HELIX 4 AA4 HIS A 284 PHE A 288 5 5 HELIX 5 AA5 SER A 299 GLY A 310 1 12 HELIX 6 AA6 GLU A 312 SER A 314 5 3 HELIX 7 AA7 PRO A 333 GLY A 342 1 10 HELIX 8 AA8 PRO A 361 LEU A 373 1 13 HELIX 9 AA9 ASN A 392 LEU A 402 1 11 HELIX 10 AB1 LYS A 416 ALA A 423 1 8 HELIX 11 AB2 GLY A 432 ARG A 442 1 11 HELIX 12 AB3 GLY A 458 GLU A 465 1 8 HELIX 13 AB4 SER A 474 PHE A 486 1 13 HELIX 14 AB5 ALA A 489 ALA A 504 1 16 HELIX 15 AB6 GLU A 507 ARG A 521 1 15 SHEET 1 AA1 6 GLN A 175 ILE A 178 0 SHEET 2 AA1 6 LYS A 143 LEU A 147 1 N ILE A 146 O PHE A 177 SHEET 3 AA1 6 ILE A 246 SER A 249 1 O ILE A 248 N LEU A 145 SHEET 4 AA1 6 VAL A 272 VAL A 276 1 O THR A 274 N ILE A 247 SHEET 5 AA1 6 ARG A 294 TYR A 296 1 O TYR A 296 N THR A 275 SHEET 6 AA1 6 ILE A 316 LYS A 317 1 O LYS A 317 N CYS A 295 SHEET 1 AA2 6 VAL A 408 LYS A 411 0 SHEET 2 AA2 6 GLN A 384 ILE A 388 1 N ILE A 387 O GLN A 409 SHEET 3 AA2 6 ALA A 349 MET A 353 1 N LEU A 352 O LEU A 386 SHEET 4 AA2 6 CYS A 426 THR A 429 1 O ILE A 428 N LEU A 351 SHEET 5 AA2 6 ILE A 446 LEU A 448 1 O ILE A 447 N ILE A 427 SHEET 6 AA2 6 GLY A 469 PHE A 471 1 O LYS A 470 N LEU A 448 SHEET 1 AA3 2 TYR A 374 ASP A 375 0 SHEET 2 AA3 2 GLU A 380 ALA A 381 -1 O GLU A 380 N ASP A 375 SITE 1 AC1 17 HIS A 155 ARG A 324 GLY A 355 ILE A 388 SITE 2 AC1 17 GLY A 390 GLY A 412 PHE A 413 ILE A 414 SITE 3 AC1 17 MET A 417 LYS A 430 GLY A 432 PRO A 433 SITE 4 AC1 17 GLY A 434 THR A 435 GLU A 438 GLU A 456 SITE 5 AC1 17 HOH A 725 SITE 1 AC2 6 TYR A 319 LYS A 505 PRO A 506 GLU A 507 SITE 2 AC2 6 ALA A 508 LYS A 511 SITE 1 AC3 4 GLU A 363 ALA A 364 ARG A 367 HOH A 702 SITE 1 AC4 3 LYS A 394 SER A 397 LYS A 398 SITE 1 AC5 5 GLU A 336 PHE A 471 GLU A 477 ILE A 481 SITE 2 AC5 5 HOH A 719 SITE 1 AC6 6 THR A 313 ALA A 372 LYS A 480 ALA A 483 SITE 2 AC6 6 HOH A 715 HOH A 738 SITE 1 AC7 6 LYS A 317 VAL A 382 ALA A 483 PHE A 486 SITE 2 AC7 6 GLY A 487 EDO A 610 SITE 1 AC8 4 SER A 397 SER A 400 SER A 401 EDO A 609 SITE 1 AC9 6 ALA A 368 ASP A 371 ALA A 372 SER A 479 SITE 2 AC9 6 EDO A 608 HOH A 738 SITE 1 AD1 6 ILE A 316 LYS A 317 VAL A 318 GLY A 487 SITE 2 AD1 6 PRO A 488 EDO A 607 CRYST1 139.250 139.250 38.270 90.00 90.00 120.00 P 63 6 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 0.007181 0.004146 0.000000 0.00000 SCALE2 0.000000 0.008292 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026130 0.00000