HEADER ISOMERASE 05-JAN-16 5HDM TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA GLUTAMATE-1-SEMIALDEHYDE-2, TITLE 2 1-AMINOMUTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE 1, CHLOROPLASTIC; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 41-474; COMPND 5 SYNONYM: ATGSA1,GSA 1,GLUTAMATE-1-SEMIALDEHYDE AMINOTRANSFERASE 1, COMPND 6 GSA-AT 1; COMPND 7 EC: 5.4.3.8; COMPND 8 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: GSA1, HEML1, AT5G63570, MBK5.3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARABIDOPSIS THALIANA, GLUTAMATE-1-SEMIALDEHYDE-2, 1-AMINOMUTASE, PMP, KEYWDS 2 PLP, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.SONG,H.PU,L.LIU REVDAT 3 08-NOV-23 5HDM 1 REMARK REVDAT 2 01-JAN-20 5HDM 1 JRNL REMARK REVDAT 1 15-JUN-16 5HDM 0 JRNL AUTH Y.SONG,H.PU,T.JIANG,L.ZHANG,M.OUYANG JRNL TITL CRYSTAL STRUCTURE OF JRNL TITL 2 GLUTAMATE-1-SEMIALDEHYDE-2,1-AMINOMUTASE FROM ARABIDOPSIS JRNL TITL 3 THALIANA. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 72 448 2016 JRNL REFN ESSN 2053-230X JRNL PMID 27303897 JRNL DOI 10.1107/S2053230X16007263 REMARK 2 REMARK 2 RESOLUTION. 1.25 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 204630 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 10210 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 28.8832 - 3.8796 0.82 6183 345 0.1508 0.1612 REMARK 3 2 3.8796 - 3.0805 0.91 6607 317 0.1275 0.1315 REMARK 3 3 3.0805 - 2.6914 0.91 6572 340 0.1390 0.1476 REMARK 3 4 2.6914 - 2.4455 0.93 6598 390 0.1324 0.1440 REMARK 3 5 2.4455 - 2.2703 0.94 6673 363 0.1256 0.1438 REMARK 3 6 2.2703 - 2.1365 0.94 6756 322 0.1189 0.1424 REMARK 3 7 2.1365 - 2.0295 0.95 6741 358 0.1174 0.1465 REMARK 3 8 2.0295 - 1.9412 0.95 6788 344 0.1171 0.1564 REMARK 3 9 1.9412 - 1.8665 0.96 6781 355 0.1130 0.1441 REMARK 3 10 1.8665 - 1.8021 0.96 6805 350 0.1137 0.1495 REMARK 3 11 1.8021 - 1.7457 0.96 6799 344 0.1102 0.1427 REMARK 3 12 1.7457 - 1.6958 0.96 6772 384 0.1090 0.1424 REMARK 3 13 1.6958 - 1.6512 0.96 6785 360 0.1044 0.1506 REMARK 3 14 1.6512 - 1.6109 0.97 6863 357 0.1045 0.1592 REMARK 3 15 1.6109 - 1.5743 0.96 6801 346 0.1026 0.1478 REMARK 3 16 1.5743 - 1.5408 0.97 6806 371 0.1061 0.1503 REMARK 3 17 1.5408 - 1.5100 0.96 6848 367 0.1064 0.1509 REMARK 3 18 1.5100 - 1.4815 0.97 6717 399 0.1139 0.1499 REMARK 3 19 1.4815 - 1.4550 0.97 6814 328 0.1205 0.1617 REMARK 3 20 1.4550 - 1.4304 0.96 6825 332 0.1214 0.1688 REMARK 3 21 1.4304 - 1.4073 0.96 6759 358 0.1238 0.1522 REMARK 3 22 1.4073 - 1.3856 0.95 6706 321 0.1270 0.1551 REMARK 3 23 1.3856 - 1.3653 0.93 6541 338 0.1268 0.1702 REMARK 3 24 1.3653 - 1.3460 0.92 6498 324 0.1314 0.1654 REMARK 3 25 1.3460 - 1.3278 0.89 6260 345 0.1324 0.1731 REMARK 3 26 1.3278 - 1.3106 0.86 6048 313 0.1356 0.1742 REMARK 3 27 1.3106 - 1.2942 0.83 5806 322 0.1449 0.1987 REMARK 3 28 1.2942 - 1.2786 0.78 5515 272 0.1458 0.1917 REMARK 3 29 1.2786 - 1.2637 0.73 5152 294 0.1476 0.1817 REMARK 3 30 1.2637 - 1.2495 0.66 4601 251 0.1649 0.2077 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.49 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 6944 REMARK 3 ANGLE : 1.091 9466 REMARK 3 CHIRALITY : 0.084 1037 REMARK 3 PLANARITY : 0.008 1242 REMARK 3 DIHEDRAL : 13.624 2614 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 5HDM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216866. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 212729 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 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 (%) : 95.0 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 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: 2GSA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM BROMIDE, PEG 2000 MME, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 32.05850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.75100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.66550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.75100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.05850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.66550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL 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 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 VAL A 1 REMARK 465 ASP A 2 REMARK 465 GLU A 3 REMARK 465 LYS A 4 REMARK 465 LYS A 5 REMARK 465 LYS A 6 REMARK 465 VAL B 1 REMARK 465 ASP B 2 REMARK 465 GLU B 3 REMARK 465 LYS B 4 REMARK 465 LYS B 5 REMARK 465 LYS B 6 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 767 O HOH B 1073 2.01 REMARK 500 CD LYS A 325 O HOH A 950 2.02 REMARK 500 O HOH A 967 O HOH B 1021 2.05 REMARK 500 O HOH B 1038 O HOH B 1100 2.08 REMARK 500 O HOH B 775 O HOH B 987 2.09 REMARK 500 O HOH B 829 O HOH B 1016 2.10 REMARK 500 O HOH A 764 O HOH A 991 2.11 REMARK 500 O HOH A 1007 O HOH B 608 2.11 REMARK 500 O HOH B 649 O HOH B 992 2.12 REMARK 500 O HOH A 685 O HOH A 976 2.13 REMARK 500 O HOH B 609 O HOH B 692 2.14 REMARK 500 CD2 LEU B 307 O HOH B 973 2.14 REMARK 500 O HOH A 685 O HOH A 940 2.15 REMARK 500 O HOH B 702 O HOH B 920 2.16 REMARK 500 O HOH A 941 O HOH A 1099 2.16 REMARK 500 O HOH A 968 O HOH A 978 2.16 REMARK 500 O HOH A 612 O HOH A 1078 2.17 REMARK 500 O HOH A 927 O HOH A 963 2.17 REMARK 500 O HOH A 633 O HOH A 951 2.17 REMARK 500 O HOH A 951 O HOH B 971 2.17 REMARK 500 O HOH B 662 O HOH B 963 2.17 REMARK 500 O HOH B 701 O HOH B 1007 2.18 REMARK 500 O HOH A 927 O HOH B 936 2.19 REMARK 500 O HOH B 923 O HOH B 1118 2.19 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 1054 O HOH B 1087 2674 2.15 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 TRP A 68 21.22 80.04 REMARK 500 ALA A 71 38.86 -85.74 REMARK 500 VAL A 166 -67.93 -125.54 REMARK 500 LYS A 274 -97.05 64.61 REMARK 500 LYS A 274 -98.75 67.59 REMARK 500 LYS A 274 -98.93 61.22 REMARK 500 SER A 361 -122.31 46.75 REMARK 500 SER A 361 -124.68 50.69 REMARK 500 SER A 404 145.89 -171.07 REMARK 500 ALA B 71 36.53 -86.67 REMARK 500 LYS B 274 -98.88 46.38 REMARK 500 LYS B 274 -97.72 62.67 REMARK 500 LYS B 274 -101.49 56.68 REMARK 500 SER B 361 -121.06 44.28 REMARK 500 SER B 361 -123.26 47.99 REMARK 500 SER B 404 145.54 -171.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1141 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A1142 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A1143 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A1144 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A1145 DISTANCE = 7.21 ANGSTROMS REMARK 525 HOH B1144 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B1145 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH B1146 DISTANCE = 6.62 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PMP A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PMP B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP B 501 and LYS B REMARK 800 274 DBREF 5HDM A 1 434 UNP P42799 GSA1_ARATH 41 474 DBREF 5HDM B 1 434 UNP P42799 GSA1_ARATH 41 474 SEQRES 1 A 434 VAL ASP GLU LYS LYS LYS SER PHE SER LEU GLN LYS SER SEQRES 2 A 434 GLU GLU ALA PHE ASN ALA ALA LYS ASN LEU MET PRO GLY SEQRES 3 A 434 GLY VAL ASN SER PRO VAL ARG ALA PHE LYS SER VAL GLY SEQRES 4 A 434 GLY GLN PRO VAL LEU ILE ASP SER VAL LYS GLY SER LYS SEQRES 5 A 434 MET TRP ASP ILE ASP GLY ASN GLU TYR ILE ASP TYR VAL SEQRES 6 A 434 GLY SER TRP GLY PRO ALA ILE ILE GLY HIS ALA ASP ASP SEQRES 7 A 434 GLU VAL LEU ALA ALA LEU ALA GLU THR MET LYS LYS GLY SEQRES 8 A 434 THR SER PHE GLY ALA PRO CYS LEU LEU GLU ASN VAL LEU SEQRES 9 A 434 ALA GLU MET VAL ILE SER ALA VAL PRO SER ILE GLU MET SEQRES 10 A 434 VAL ARG PHE VAL ASN SER GLY THR GLU ALA CYS MET GLY SEQRES 11 A 434 VAL LEU ARG LEU ALA ARG ALA PHE THR ASN LYS GLU LYS SEQRES 12 A 434 PHE ILE LYS PHE GLU GLY CYS TYR HIS GLY HIS ALA ASN SEQRES 13 A 434 ALA PHE LEU VAL LYS ALA GLY SER GLY VAL ALA THR LEU SEQRES 14 A 434 GLY LEU PRO ASP SER PRO GLY VAL PRO LYS ALA ALA THR SEQRES 15 A 434 SER ASP THR LEU THR ALA PRO TYR ASN ASP LEU GLU ALA SEQRES 16 A 434 VAL GLU LYS LEU PHE ALA ALA HIS LYS GLY GLU ILE SER SEQRES 17 A 434 ALA VAL ILE LEU GLU PRO VAL VAL GLY ASN SER GLY PHE SEQRES 18 A 434 ILE PRO PRO THR PRO GLU PHE ILE ASN GLY LEU ARG GLN SEQRES 19 A 434 LEU THR LYS ASP ASN GLY VAL LEU LEU ILE PHE ASP GLU SEQRES 20 A 434 VAL MET THR GLY PHE ARG LEU ALA TYR GLY GLY ALA GLN SEQRES 21 A 434 GLU TYR PHE GLY ILE THR PRO ASP LEU THR THR LEU GLY SEQRES 22 A 434 LYS ILE ILE GLY GLY GLY LEU PRO VAL GLY ALA TYR GLY SEQRES 23 A 434 GLY ARG ARG ASP ILE MET GLU MET VAL ALA PRO ALA GLY SEQRES 24 A 434 PRO MET TYR GLN ALA GLY THR LEU SER GLY ASN PRO LEU SEQRES 25 A 434 ALA MET THR ALA GLY ILE HIS THR LEU LYS ARG LEU LYS SEQRES 26 A 434 GLN ALA GLY THR TYR GLU TYR LEU ASP LYS ILE THR LYS SEQRES 27 A 434 GLU LEU THR ASN GLY ILE LEU GLU ALA GLY LYS LYS THR SEQRES 28 A 434 GLY HIS PRO MET CYS GLY GLY TYR ILE SER GLY MET PHE SEQRES 29 A 434 GLY PHE PHE PHE ALA GLU GLY PRO VAL TYR ASN PHE ALA SEQRES 30 A 434 ASP SER LYS LYS SER ASP THR GLU LYS PHE GLY ARG PHE SEQRES 31 A 434 PHE ARG GLY MET LEU GLU GLU GLY VAL TYR PHE ALA PRO SEQRES 32 A 434 SER GLN PHE GLU ALA GLY PHE THR SER LEU ALA HIS THR SEQRES 33 A 434 PRO GLU ASP ILE GLN LEU THR ILE ALA ALA ALA GLU ARG SEQRES 34 A 434 VAL LEU SER ARG ILE SEQRES 1 B 434 VAL ASP GLU LYS LYS LYS SER PHE SER LEU GLN LYS SER SEQRES 2 B 434 GLU GLU ALA PHE ASN ALA ALA LYS ASN LEU MET PRO GLY SEQRES 3 B 434 GLY VAL ASN SER PRO VAL ARG ALA PHE LYS SER VAL GLY SEQRES 4 B 434 GLY GLN PRO VAL LEU ILE ASP SER VAL LYS GLY SER LYS SEQRES 5 B 434 MET TRP ASP ILE ASP GLY ASN GLU TYR ILE ASP TYR VAL SEQRES 6 B 434 GLY SER TRP GLY PRO ALA ILE ILE GLY HIS ALA ASP ASP SEQRES 7 B 434 GLU VAL LEU ALA ALA LEU ALA GLU THR MET LYS LYS GLY SEQRES 8 B 434 THR SER PHE GLY ALA PRO CYS LEU LEU GLU ASN VAL LEU SEQRES 9 B 434 ALA GLU MET VAL ILE SER ALA VAL PRO SER ILE GLU MET SEQRES 10 B 434 VAL ARG PHE VAL ASN SER GLY THR GLU ALA CYS MET GLY SEQRES 11 B 434 VAL LEU ARG LEU ALA ARG ALA PHE THR ASN LYS GLU LYS SEQRES 12 B 434 PHE ILE LYS PHE GLU GLY CYS TYR HIS GLY HIS ALA ASN SEQRES 13 B 434 ALA PHE LEU VAL LYS ALA GLY SER GLY VAL ALA THR LEU SEQRES 14 B 434 GLY LEU PRO ASP SER PRO GLY VAL PRO LYS ALA ALA THR SEQRES 15 B 434 SER ASP THR LEU THR ALA PRO TYR ASN ASP LEU GLU ALA SEQRES 16 B 434 VAL GLU LYS LEU PHE ALA ALA HIS LYS GLY GLU ILE SER SEQRES 17 B 434 ALA VAL ILE LEU GLU PRO VAL VAL GLY ASN SER GLY PHE SEQRES 18 B 434 ILE PRO PRO THR PRO GLU PHE ILE ASN GLY LEU ARG GLN SEQRES 19 B 434 LEU THR LYS ASP ASN GLY VAL LEU LEU ILE PHE ASP GLU SEQRES 20 B 434 VAL MET THR GLY PHE ARG LEU ALA TYR GLY GLY ALA GLN SEQRES 21 B 434 GLU TYR PHE GLY ILE THR PRO ASP LEU THR THR LEU GLY SEQRES 22 B 434 LYS ILE ILE GLY GLY GLY LEU PRO VAL GLY ALA TYR GLY SEQRES 23 B 434 GLY ARG ARG ASP ILE MET GLU MET VAL ALA PRO ALA GLY SEQRES 24 B 434 PRO MET TYR GLN ALA GLY THR LEU SER GLY ASN PRO LEU SEQRES 25 B 434 ALA MET THR ALA GLY ILE HIS THR LEU LYS ARG LEU LYS SEQRES 26 B 434 GLN ALA GLY THR TYR GLU TYR LEU ASP LYS ILE THR LYS SEQRES 27 B 434 GLU LEU THR ASN GLY ILE LEU GLU ALA GLY LYS LYS THR SEQRES 28 B 434 GLY HIS PRO MET CYS GLY GLY TYR ILE SER GLY MET PHE SEQRES 29 B 434 GLY PHE PHE PHE ALA GLU GLY PRO VAL TYR ASN PHE ALA SEQRES 30 B 434 ASP SER LYS LYS SER ASP THR GLU LYS PHE GLY ARG PHE SEQRES 31 B 434 PHE ARG GLY MET LEU GLU GLU GLY VAL TYR PHE ALA PRO SEQRES 32 B 434 SER GLN PHE GLU ALA GLY PHE THR SER LEU ALA HIS THR SEQRES 33 B 434 PRO GLU ASP ILE GLN LEU THR ILE ALA ALA ALA GLU ARG SEQRES 34 B 434 VAL LEU SER ARG ILE HET PMP A 500 16 HET PLP B 501 15 HET PMP B 502 16 HETNAM PMP 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PMP PYRIDOXAMINE-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 PMP 2(C8 H13 N2 O5 P) FORMUL 4 PLP C8 H10 N O6 P FORMUL 6 HOH *1091(H2 O) HELIX 1 AA1 LEU A 10 LYS A 21 1 12 HELIX 2 AA2 ASN A 22 LEU A 23 5 2 HELIX 3 AA3 MET A 24 VAL A 28 5 5 HELIX 4 AA4 SER A 30 GLY A 39 5 10 HELIX 5 AA5 VAL A 65 GLY A 69 5 5 HELIX 6 AA6 ASP A 77 LYS A 89 1 13 HELIX 7 AA7 CYS A 98 VAL A 112 1 15 HELIX 8 AA8 SER A 123 ASN A 140 1 18 HELIX 9 AA9 ALA A 155 LEU A 159 5 5 HELIX 10 AB1 PRO A 178 SER A 183 1 6 HELIX 11 AB2 ASP A 192 HIS A 203 1 12 HELIX 12 AB3 THR A 225 ASN A 239 1 15 HELIX 13 AB4 GLY A 257 GLY A 264 1 8 HELIX 14 AB5 ILE A 275 GLY A 278 5 4 HELIX 15 AB6 ARG A 288 GLU A 293 1 6 HELIX 16 AB7 ASN A 310 LYS A 325 1 16 HELIX 17 AB8 GLY A 328 THR A 351 1 24 HELIX 18 AB9 ASN A 375 LYS A 380 1 6 HELIX 19 AC1 ASP A 383 GLU A 397 1 15 HELIX 20 AC2 THR A 416 SER A 432 1 17 HELIX 21 AC3 LEU B 10 LYS B 21 1 12 HELIX 22 AC4 ASN B 22 LEU B 23 5 2 HELIX 23 AC5 MET B 24 VAL B 28 5 5 HELIX 24 AC6 SER B 30 GLY B 39 5 10 HELIX 25 AC7 VAL B 65 GLY B 69 5 5 HELIX 26 AC8 ASP B 77 LYS B 89 1 13 HELIX 27 AC9 CYS B 98 VAL B 112 1 15 HELIX 28 AD1 SER B 123 ASN B 140 1 18 HELIX 29 AD2 ALA B 155 LEU B 159 5 5 HELIX 30 AD3 PRO B 178 SER B 183 1 6 HELIX 31 AD4 ASP B 192 HIS B 203 1 12 HELIX 32 AD5 THR B 225 ASN B 239 1 15 HELIX 33 AD6 GLY B 257 GLY B 264 1 8 HELIX 34 AD7 ILE B 275 GLY B 278 5 4 HELIX 35 AD8 ARG B 288 GLU B 293 1 6 HELIX 36 AD9 ASN B 310 LYS B 325 1 16 HELIX 37 AE1 GLY B 328 THR B 351 1 24 HELIX 38 AE2 ASN B 375 LYS B 380 1 6 HELIX 39 AE3 ASP B 383 GLU B 397 1 15 HELIX 40 AE4 THR B 416 SER B 432 1 17 SHEET 1 AA1 4 ILE A 45 LYS A 49 0 SHEET 2 AA1 4 LYS A 52 ASP A 55 -1 O TRP A 54 N SER A 47 SHEET 3 AA1 4 GLU A 60 ASP A 63 -1 O TYR A 61 N MET A 53 SHEET 4 AA1 4 VAL A 399 TYR A 400 1 O TYR A 400 N ILE A 62 SHEET 1 AA2 7 MET A 117 VAL A 121 0 SHEET 2 AA2 7 GLY A 283 GLY A 287 -1 O GLY A 283 N VAL A 121 SHEET 3 AA2 7 LEU A 269 GLY A 273 -1 N THR A 270 O GLY A 286 SHEET 4 AA2 7 LEU A 242 ASP A 246 1 N PHE A 245 O LEU A 269 SHEET 5 AA2 7 ILE A 207 LEU A 212 1 N VAL A 210 O ILE A 244 SHEET 6 AA2 7 LYS A 143 GLU A 148 1 N LYS A 143 O SER A 208 SHEET 7 AA2 7 THR A 185 PRO A 189 1 O LEU A 186 N PHE A 144 SHEET 1 AA3 3 CYS A 356 ILE A 360 0 SHEET 2 AA3 3 MET A 363 PHE A 367 -1 O PHE A 367 N CYS A 356 SHEET 3 AA3 3 GLY A 409 PHE A 410 -1 O GLY A 409 N PHE A 364 SHEET 1 AA4 4 ILE B 45 LYS B 49 0 SHEET 2 AA4 4 LYS B 52 ASP B 55 -1 O TRP B 54 N SER B 47 SHEET 3 AA4 4 GLU B 60 ASP B 63 -1 O TYR B 61 N MET B 53 SHEET 4 AA4 4 VAL B 399 TYR B 400 1 O TYR B 400 N ILE B 62 SHEET 1 AA5 7 MET B 117 VAL B 121 0 SHEET 2 AA5 7 GLY B 283 GLY B 287 -1 O GLY B 283 N VAL B 121 SHEET 3 AA5 7 LEU B 269 GLY B 273 -1 N THR B 270 O GLY B 286 SHEET 4 AA5 7 LEU B 242 ASP B 246 1 N PHE B 245 O LEU B 269 SHEET 5 AA5 7 ILE B 207 LEU B 212 1 N VAL B 210 O ILE B 244 SHEET 6 AA5 7 LYS B 143 GLU B 148 1 N LYS B 143 O SER B 208 SHEET 7 AA5 7 THR B 185 PRO B 189 1 O LEU B 186 N PHE B 144 SHEET 1 AA6 3 CYS B 356 ILE B 360 0 SHEET 2 AA6 3 MET B 363 PHE B 367 -1 O PHE B 367 N CYS B 356 SHEET 3 AA6 3 GLY B 409 PHE B 410 -1 O GLY B 409 N PHE B 364 LINK NZ BLYS A 274 N4A PMP A 500 1555 1555 1.18 LINK NZ ALYS B 274 C4AAPLP B 501 1555 1555 1.38 CISPEP 1 ALA A 296 PRO A 297 0 7.33 CISPEP 2 GLY A 371 PRO A 372 0 1.02 CISPEP 3 ALA B 296 PRO B 297 0 8.64 CISPEP 4 GLY B 371 PRO B 372 0 1.94 SITE 1 AC1 15 SER A 123 GLY A 124 THR A 125 TYR A 151 SITE 2 AC1 15 GLY A 153 GLU A 213 ASN A 218 ASP A 246 SITE 3 AC1 15 VAL A 248 MET A 249 LYS A 274 HOH A 741 SITE 4 AC1 15 HOH A 815 THR B 306 HOH B 742 SITE 1 AC2 16 THR A 306 SER B 123 GLY B 124 THR B 125 SITE 2 AC2 16 TYR B 151 GLY B 153 GLU B 213 ASN B 218 SITE 3 AC2 16 ASP B 246 MET B 249 LYS B 274 PLP B 501 SITE 4 AC2 16 HOH B 636 HOH B 676 HOH B 710 HOH B 799 SITE 1 AC3 24 THR A 306 TRP B 68 PRO B 70 SER B 123 SITE 2 AC3 24 GLY B 124 THR B 125 TYR B 151 GLU B 213 SITE 3 AC3 24 ASN B 218 ASP B 246 VAL B 248 MET B 249 SITE 4 AC3 24 GLY B 273 ILE B 275 ILE B 276 GLY B 277 SITE 5 AC3 24 GLY B 278 VAL B 282 PMP B 502 HOH B 676 SITE 6 AC3 24 HOH B 691 HOH B 710 HOH B 799 HOH B 883 CRYST1 64.117 109.331 115.502 90.00 90.00 90.00 P 21 21 21 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 0.015596 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009147 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008658 0.00000