PDB Short entry for 2YOB HEADER TRANSFERASE 22-OCT-12 2YOB TITLE HIGH RESOLUTION AGXT_M STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE--PYRUVATE AMINOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SPT, ALANINE--GLYOXYLATE AMINOTRANSFERASE, AGT; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCOLDII KEYWDS TRANSFERASE, PRIMARY HYPEROXALURIA TYPE I, AGXT FOLDING AND STABILITY KEYWDS 2 DEFECTS EXPDTA X-RAY DIFFRACTION AUTHOR I.FABELO-ROSA,N.MESA-TORRES,D.RIVEROL,C.YUNTA,A.ALBERT,E.SALIDO, AUTHOR 2 A.L.PEY REVDAT 3 20-DEC-23 2YOB 1 REMARK LINK REVDAT 2 20-NOV-13 2YOB 1 JRNL REVDAT 1 30-OCT-13 2YOB 0 JRNL AUTH N.MESA-TORRES,I.FABELO-ROSA,D.RIVEROL,C.YUNTA,A.ALBERT, JRNL AUTH 2 E.SALIDO,A.L.PEY JRNL TITL THE ROLE OF PROTEIN DENATURATION ENERGETICS AND MOLECULAR JRNL TITL 2 CHAPERONES IN THE AGGREGATION AND MISTARGETING OF MUTANTS JRNL TITL 3 CAUSING PRIMARY HYPEROXALURIA TYPE I JRNL REF PLOS ONE V. 8 71963 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 24205397 JRNL DOI 10.1371/JOURNAL.PONE.0071963 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 45.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 69358 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3507 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 45.9631 - 5.5521 0.99 2833 163 0.1632 0.1752 REMARK 3 2 5.5521 - 4.4080 1.00 2731 136 0.1356 0.1588 REMARK 3 3 4.4080 - 3.8511 1.00 2679 158 0.1368 0.1528 REMARK 3 4 3.8511 - 3.4991 1.00 2649 167 0.1577 0.1719 REMARK 3 5 3.4991 - 3.2484 1.00 2658 131 0.1635 0.2201 REMARK 3 6 3.2484 - 3.0569 1.00 2663 146 0.1664 0.1974 REMARK 3 7 3.0569 - 2.9038 1.00 2626 163 0.1685 0.2302 REMARK 3 8 2.9038 - 2.7775 1.00 2635 144 0.1686 0.1888 REMARK 3 9 2.7775 - 2.6705 1.00 2651 139 0.1649 0.2288 REMARK 3 10 2.6705 - 2.5784 1.00 2610 128 0.1577 0.2001 REMARK 3 11 2.5784 - 2.4978 1.00 2627 147 0.1629 0.2090 REMARK 3 12 2.4978 - 2.4264 1.00 2648 128 0.1636 0.2259 REMARK 3 13 2.4264 - 2.3625 1.00 2612 133 0.1635 0.2094 REMARK 3 14 2.3625 - 2.3049 1.00 2615 159 0.1691 0.2117 REMARK 3 15 2.3049 - 2.2525 1.00 2607 125 0.2088 0.3025 REMARK 3 16 2.2525 - 2.2045 1.00 2602 142 0.2291 0.2806 REMARK 3 17 2.2045 - 2.1604 1.00 2624 139 0.1822 0.2325 REMARK 3 18 2.1604 - 2.1197 1.00 2602 137 0.1689 0.2261 REMARK 3 19 2.1197 - 2.0818 1.00 2615 138 0.1675 0.2044 REMARK 3 20 2.0818 - 2.0465 1.00 2627 128 0.1812 0.2560 REMARK 3 21 2.0465 - 2.0135 1.00 2587 128 0.2025 0.2563 REMARK 3 22 2.0135 - 1.9825 1.00 2628 144 0.2221 0.2586 REMARK 3 23 1.9825 - 1.9534 1.00 2546 140 0.2514 0.3394 REMARK 3 24 1.9534 - 1.9259 1.00 2654 125 0.2999 0.3002 REMARK 3 25 1.9259 - 1.8998 0.96 2522 119 0.3180 0.3399 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 34.75 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.96460 REMARK 3 B22 (A**2) : -4.85760 REMARK 3 B33 (A**2) : -0.10700 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 6160 REMARK 3 ANGLE : 1.064 8348 REMARK 3 CHIRALITY : 0.072 924 REMARK 3 PLANARITY : 0.005 1062 REMARK 3 DIHEDRAL : 17.236 2316 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -9.5159 14.9471 -38.9801 REMARK 3 T TENSOR REMARK 3 T11: 0.0151 T22: 0.0671 REMARK 3 T33: 0.0946 T12: 0.0053 REMARK 3 T13: -0.0465 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 0.3308 L22: 1.3060 REMARK 3 L33: 1.1941 L12: -0.0010 REMARK 3 L13: -0.1869 L23: -0.0183 REMARK 3 S TENSOR REMARK 3 S11: 0.0152 S12: 0.0059 S13: -0.0024 REMARK 3 S21: -0.1744 S22: 0.0235 S23: 0.2083 REMARK 3 S31: -0.0025 S32: -0.0365 S33: -0.0115 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 2YOB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1290054509. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-SEP-11 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 : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.94 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69440 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 48.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 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: PDB ENTRY 1H0C REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 3350, 0.1M BIS-TRIS PH 5.2, REMARK 280 150MM LI2SO4 AND 5% W/V OCTYL-B-D-GLUCOSIDE 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 27.24750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.91600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.76250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.91600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.24750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.76250 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: 11840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.4 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 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 A 2120 O HOH A 2226 2.18 REMARK 500 O HOH A 2047 O HOH B 2308 2.19 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 209 -114.94 -93.33 REMARK 500 LYS B 5 -159.87 -79.96 REMARK 500 LYS B 147 62.06 38.57 REMARK 500 LYS B 209 -120.42 -94.56 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 A2178 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH B2029 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH B2308 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH B2309 DISTANCE = 5.85 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 PYRIDOXAL-5'-PHOSPHATE (PLP): SCHIFF BASE WITH K209 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 1389 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 1389 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTB A 1390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTB B 1391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1392 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1393 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1394 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1392 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1395 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1393 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H0C RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF HUMAN ALANINE:GLYOXYLATE AMINTRANSFERASE. REMARK 900 RELATED ID: 1J04 RELATED DB: PDB REMARK 900 STRUCTURAL MECHANISM OF ENZYME MISTARGETING IN HEREDITARYKIDNEY REMARK 900 STONE DISEASE IN VITRO DBREF 2YOB A 1 388 UNP P21549 SPYA_HUMAN 1 388 DBREF 2YOB B 1 388 UNP P21549 SPYA_HUMAN 1 388 SEQADV 2YOB MET A 340 UNP P21549 ILE 340 ENGINEERED MUTATION SEQADV 2YOB VAL A 385 UNP P21549 GLN 385 ENGINEERED MUTATION SEQADV 2YOB ALA A 386 UNP P21549 HIS 386 ENGINEERED MUTATION SEQADV 2YOB GLN A 387 UNP P21549 CYS 387 ENGINEERED MUTATION SEQADV 2YOB ALA A 388 UNP P21549 PRO 388 ENGINEERED MUTATION SEQADV 2YOB MET B 340 UNP P21549 ILE 340 ENGINEERED MUTATION SEQADV 2YOB VAL B 385 UNP P21549 GLN 385 ENGINEERED MUTATION SEQADV 2YOB ALA B 386 UNP P21549 HIS 386 ENGINEERED MUTATION SEQADV 2YOB GLN B 387 UNP P21549 CYS 387 ENGINEERED MUTATION SEQADV 2YOB ALA B 388 UNP P21549 PRO 388 ENGINEERED MUTATION SEQRES 1 A 388 MET ALA SER HIS LYS LEU LEU VAL THR PRO PRO LYS ALA SEQRES 2 A 388 LEU LEU LYS PRO LEU SER ILE PRO ASN GLN LEU LEU LEU SEQRES 3 A 388 GLY PRO GLY PRO SER ASN LEU PRO PRO ARG ILE MET ALA SEQRES 4 A 388 ALA GLY GLY LEU GLN MET ILE GLY SER MET SER LYS ASP SEQRES 5 A 388 MET TYR GLN ILE MET ASP GLU ILE LYS GLU GLY ILE GLN SEQRES 6 A 388 TYR VAL PHE GLN THR ARG ASN PRO LEU THR LEU VAL ILE SEQRES 7 A 388 SER GLY SER GLY HIS CYS ALA LEU GLU ALA ALA LEU VAL SEQRES 8 A 388 ASN VAL LEU GLU PRO GLY ASP SER PHE LEU VAL GLY ALA SEQRES 9 A 388 ASN GLY ILE TRP GLY GLN ARG ALA VAL ASP ILE GLY GLU SEQRES 10 A 388 ARG ILE GLY ALA ARG VAL HIS PRO MET THR LYS ASP PRO SEQRES 11 A 388 GLY GLY HIS TYR THR LEU GLN GLU VAL GLU GLU GLY LEU SEQRES 12 A 388 ALA GLN HIS LYS PRO VAL LEU LEU PHE LEU THR HIS GLY SEQRES 13 A 388 GLU SER SER THR GLY VAL LEU GLN PRO LEU ASP GLY PHE SEQRES 14 A 388 GLY GLU LEU CYS HIS ARG TYR LYS CYS LEU LEU LEU VAL SEQRES 15 A 388 ASP SER VAL ALA SER LEU GLY GLY THR PRO LEU TYR MET SEQRES 16 A 388 ASP ARG GLN GLY ILE ASP ILE LEU TYR SER GLY SER GLN SEQRES 17 A 388 LYS ALA LEU ASN ALA PRO PRO GLY THR SER LEU ILE SER SEQRES 18 A 388 PHE SER ASP LYS ALA LYS LYS LYS MET TYR SER ARG LYS SEQRES 19 A 388 THR LYS PRO PHE SER PHE TYR LEU ASP ILE LYS TRP LEU SEQRES 20 A 388 ALA ASN PHE TRP GLY CYS ASP ASP GLN PRO ARG MET TYR SEQRES 21 A 388 HIS HIS THR ILE PRO VAL ILE SER LEU TYR SER LEU ARG SEQRES 22 A 388 GLU SER LEU ALA LEU ILE ALA GLU GLN GLY LEU GLU ASN SEQRES 23 A 388 SER TRP ARG GLN HIS ARG GLU ALA ALA ALA TYR LEU HIS SEQRES 24 A 388 GLY ARG LEU GLN ALA LEU GLY LEU GLN LEU PHE VAL LYS SEQRES 25 A 388 ASP PRO ALA LEU ARG LEU PRO THR VAL THR THR VAL ALA SEQRES 26 A 388 VAL PRO ALA GLY TYR ASP TRP ARG ASP ILE VAL SER TYR SEQRES 27 A 388 VAL MET ASP HIS PHE ASP ILE GLU ILE MET GLY GLY LEU SEQRES 28 A 388 GLY PRO SER THR GLY LYS VAL LEU ARG ILE GLY LEU LEU SEQRES 29 A 388 GLY CYS ASN ALA THR ARG GLU ASN VAL ASP ARG VAL THR SEQRES 30 A 388 GLU ALA LEU ARG ALA ALA LEU VAL ALA GLN ALA SEQRES 1 B 388 MET ALA SER HIS LYS LEU LEU VAL THR PRO PRO LYS ALA SEQRES 2 B 388 LEU LEU LYS PRO LEU SER ILE PRO ASN GLN LEU LEU LEU SEQRES 3 B 388 GLY PRO GLY PRO SER ASN LEU PRO PRO ARG ILE MET ALA SEQRES 4 B 388 ALA GLY GLY LEU GLN MET ILE GLY SER MET SER LYS ASP SEQRES 5 B 388 MET TYR GLN ILE MET ASP GLU ILE LYS GLU GLY ILE GLN SEQRES 6 B 388 TYR VAL PHE GLN THR ARG ASN PRO LEU THR LEU VAL ILE SEQRES 7 B 388 SER GLY SER GLY HIS CYS ALA LEU GLU ALA ALA LEU VAL SEQRES 8 B 388 ASN VAL LEU GLU PRO GLY ASP SER PHE LEU VAL GLY ALA SEQRES 9 B 388 ASN GLY ILE TRP GLY GLN ARG ALA VAL ASP ILE GLY GLU SEQRES 10 B 388 ARG ILE GLY ALA ARG VAL HIS PRO MET THR LYS ASP PRO SEQRES 11 B 388 GLY GLY HIS TYR THR LEU GLN GLU VAL GLU GLU GLY LEU SEQRES 12 B 388 ALA GLN HIS LYS PRO VAL LEU LEU PHE LEU THR HIS GLY SEQRES 13 B 388 GLU SER SER THR GLY VAL LEU GLN PRO LEU ASP GLY PHE SEQRES 14 B 388 GLY GLU LEU CYS HIS ARG TYR LYS CYS LEU LEU LEU VAL SEQRES 15 B 388 ASP SER VAL ALA SER LEU GLY GLY THR PRO LEU TYR MET SEQRES 16 B 388 ASP ARG GLN GLY ILE ASP ILE LEU TYR SER GLY SER GLN SEQRES 17 B 388 LYS ALA LEU ASN ALA PRO PRO GLY THR SER LEU ILE SER SEQRES 18 B 388 PHE SER ASP LYS ALA LYS LYS LYS MET TYR SER ARG LYS SEQRES 19 B 388 THR LYS PRO PHE SER PHE TYR LEU ASP ILE LYS TRP LEU SEQRES 20 B 388 ALA ASN PHE TRP GLY CYS ASP ASP GLN PRO ARG MET TYR SEQRES 21 B 388 HIS HIS THR ILE PRO VAL ILE SER LEU TYR SER LEU ARG SEQRES 22 B 388 GLU SER LEU ALA LEU ILE ALA GLU GLN GLY LEU GLU ASN SEQRES 23 B 388 SER TRP ARG GLN HIS ARG GLU ALA ALA ALA TYR LEU HIS SEQRES 24 B 388 GLY ARG LEU GLN ALA LEU GLY LEU GLN LEU PHE VAL LYS SEQRES 25 B 388 ASP PRO ALA LEU ARG LEU PRO THR VAL THR THR VAL ALA SEQRES 26 B 388 VAL PRO ALA GLY TYR ASP TRP ARG ASP ILE VAL SER TYR SEQRES 27 B 388 VAL MET ASP HIS PHE ASP ILE GLU ILE MET GLY GLY LEU SEQRES 28 B 388 GLY PRO SER THR GLY LYS VAL LEU ARG ILE GLY LEU LEU SEQRES 29 B 388 GLY CYS ASN ALA THR ARG GLU ASN VAL ASP ARG VAL THR SEQRES 30 B 388 GLU ALA LEU ARG ALA ALA LEU VAL ALA GLN ALA HET PLP A1389 15 HET BTB A1390 14 HET SO4 A1391 5 HET GOL A1392 6 HET GOL A1393 6 HET GOL A1394 6 HET GOL A1395 6 HET PLP B1389 15 HET SO4 B1390 5 HET BTB B1391 14 HET GOL B1392 6 HET GOL B1393 6 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- HETNAM 2 BTB PROPANE-1,3-DIOL HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN BTB BIS-TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 4 BTB 2(C8 H19 N O5) FORMUL 5 SO4 2(O4 S 2-) FORMUL 6 GOL 6(C3 H8 O3) FORMUL 15 HOH *702(H2 O) HELIX 1 1 PRO A 11 LYS A 16 5 6 HELIX 2 2 PRO A 34 GLY A 42 1 9 HELIX 3 3 SER A 50 GLN A 69 1 20 HELIX 4 4 SER A 81 LEU A 94 1 14 HELIX 5 5 GLY A 106 ILE A 119 1 14 HELIX 6 6 THR A 135 LYS A 147 1 13 HELIX 7 7 GLY A 168 TYR A 176 1 9 HELIX 8 8 SER A 223 TYR A 231 1 9 HELIX 9 9 ASP A 243 TRP A 251 1 9 HELIX 10 10 PRO A 265 GLY A 283 1 19 HELIX 11 11 GLY A 283 LEU A 305 1 23 HELIX 12 12 ASP A 313 LEU A 316 5 4 HELIX 13 13 ASP A 331 ASP A 344 1 14 HELIX 14 14 LEU A 351 THR A 355 5 5 HELIX 15 15 LEU A 364 ALA A 368 5 5 HELIX 16 16 THR A 369 GLN A 387 1 19 HELIX 17 17 PRO B 11 LYS B 16 5 6 HELIX 18 18 PRO B 34 GLY B 42 1 9 HELIX 19 19 SER B 50 GLN B 69 1 20 HELIX 20 20 SER B 81 LEU B 94 1 14 HELIX 21 21 GLY B 106 ILE B 119 1 14 HELIX 22 22 THR B 135 LYS B 147 1 13 HELIX 23 23 GLY B 168 TYR B 176 1 9 HELIX 24 24 SER B 223 TYR B 231 1 9 HELIX 25 25 ASP B 243 TRP B 251 1 9 HELIX 26 26 PRO B 265 GLY B 283 1 19 HELIX 27 27 GLY B 283 LEU B 305 1 23 HELIX 28 28 ASP B 313 LEU B 316 5 4 HELIX 29 29 ASP B 331 ASP B 344 1 14 HELIX 30 30 LEU B 351 THR B 355 5 5 HELIX 31 31 LEU B 364 ALA B 368 5 5 HELIX 32 32 THR B 369 ALA B 388 1 20 SHEET 1 AA 2 LEU A 24 LEU A 25 0 SHEET 2 AA 2 ILE A 345 GLU A 346 1 N GLU A 346 O LEU A 24 SHEET 1 AB 7 LEU A 74 ILE A 78 0 SHEET 2 AB 7 SER A 218 PHE A 222 -1 O SER A 218 N ILE A 78 SHEET 3 AB 7 ILE A 202 GLY A 206 -1 O LEU A 203 N SER A 221 SHEET 4 AB 7 LEU A 179 ASP A 183 1 O LEU A 180 N ILE A 202 SHEET 5 AB 7 LEU A 150 THR A 154 1 O LEU A 151 N LEU A 181 SHEET 6 AB 7 SER A 99 ALA A 104 1 O LEU A 101 N PHE A 152 SHEET 7 AB 7 ARG A 122 THR A 127 1 O ARG A 122 N PHE A 100 SHEET 1 AC 2 GLY A 156 GLU A 157 0 SHEET 2 AC 2 VAL A 162 LEU A 163 -1 O VAL A 162 N GLU A 157 SHEET 1 AD 2 VAL A 321 ALA A 325 0 SHEET 2 AD 2 VAL A 358 GLY A 362 -1 O LEU A 359 N VAL A 324 SHEET 1 BA 2 LEU B 24 LEU B 25 0 SHEET 2 BA 2 ILE B 345 GLU B 346 1 N GLU B 346 O LEU B 24 SHEET 1 BB 7 LEU B 74 ILE B 78 0 SHEET 2 BB 7 SER B 218 PHE B 222 -1 O SER B 218 N ILE B 78 SHEET 3 BB 7 ILE B 202 GLY B 206 -1 O LEU B 203 N SER B 221 SHEET 4 BB 7 LEU B 179 ASP B 183 1 O LEU B 180 N ILE B 202 SHEET 5 BB 7 LEU B 150 THR B 154 1 O LEU B 151 N LEU B 181 SHEET 6 BB 7 SER B 99 ALA B 104 1 O LEU B 101 N PHE B 152 SHEET 7 BB 7 ARG B 122 THR B 127 1 O ARG B 122 N PHE B 100 SHEET 1 BC 2 GLY B 156 GLU B 157 0 SHEET 2 BC 2 VAL B 162 LEU B 163 -1 O VAL B 162 N GLU B 157 SHEET 1 BD 2 VAL B 321 ALA B 325 0 SHEET 2 BD 2 VAL B 358 GLY B 362 -1 O LEU B 359 N VAL B 324 LINK NZ LYS A 209 C4A PLP A1389 1555 1555 1.39 LINK NZ LYS B 209 C4A PLP B1389 1555 1555 1.38 CISPEP 1 GLY A 29 PRO A 30 0 -0.38 CISPEP 2 GLY B 29 PRO B 30 0 -0.98 SITE 1 AC1 13 SER A 81 GLY A 82 HIS A 83 TRP A 108 SITE 2 AC1 13 GLY A 156 SER A 158 ASP A 183 VAL A 185 SITE 3 AC1 13 ALA A 186 GLN A 208 LYS A 209 TYR B 260 SITE 4 AC1 13 THR B 263 SITE 1 AC2 13 TYR A 260 THR A 263 SER B 81 GLY B 82 SITE 2 AC2 13 HIS B 83 TRP B 108 GLY B 156 SER B 158 SITE 3 AC2 13 ASP B 183 VAL B 185 ALA B 186 GLN B 208 SITE 4 AC2 13 LYS B 209 SITE 1 AC3 6 ARG B 258 HOH B2009 HOH B2073 HOH B2231 SITE 2 AC3 6 HOH B2303 HOH B2304 SITE 1 AC4 6 TRP A 246 ASN A 249 ASP A 254 MET A 259 SITE 2 AC4 6 HOH A2288 HOH A2290 SITE 1 AC5 9 HOH A2193 LYS B 245 TRP B 246 ASN B 249 SITE 2 AC5 9 ASP B 254 GLN B 256 MET B 259 GOL B1393 SITE 3 AC5 9 HOH B2221 SITE 1 AC6 3 LYS A 5 ARG B 197 HIS B 342 SITE 1 AC7 6 ASN A 72 SER A 223 ASP A 224 HOH A2145 SITE 2 AC7 6 HOH A2260 HOH A2272 SITE 1 AC8 8 SER A 50 LYS A 51 HOH A2109 HOH A2111 SITE 2 AC8 8 HOH A2389 HOH A2390 GLN B 23 MET B 340 SITE 1 AC9 7 MET A 38 ALA A 39 GLY A 42 HOH A2092 SITE 2 AC9 7 HOH A2096 HOH A2392 GLY B 42 SITE 1 BC1 4 THR B 135 LEU B 136 HOH B2148 HOH B2307 SITE 1 BC2 8 VAL A 336 SER A 337 MET A 340 HOH A2347 SITE 2 BC2 8 HOH A2352 HOH A2356 HOH A2365 HOH A2393 SITE 1 BC3 6 HOH A2182 HOH A2193 LYS B 236 TRP B 246 SITE 2 BC3 6 BTB B1391 HOH B2220 CRYST1 54.495 103.525 153.832 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 0.018350 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009660 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006501 0.00000