HEADER HYDROLASE 16-APR-14 4CYY TITLE THE STRUCTURE OF VANIN-1: DEFINING THE LINK BETWEEN METABOLIC DISEASE, TITLE 2 OXIDATIVE STRESS AND INFLAMMATION CAVEAT 4CYY NAG B 1 HAS WRONG CHIRALITY AT ATOM C1 NAG A 532 HAS WRONG CAVEAT 2 4CYY CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PANTETHEINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PANTETHEINE HYDROLASE, TIFF66, VASCULAR NON-INFLAMMATORY COMPND 5 MOLECULE 1, VANIN-1; COMPND 6 EC: 3.5.1.92; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: FLAG-TAG AT THE N-TERMINUS AND PRO-PEPTIDE AT THE C- COMPND 9 TERMINUS HAS BEEN REMOVED TO GIVE THE MATURE FORM OF THE PROTEIN. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PAPEX-3P KEYWDS HYDROLASE, INFLAMMATION, OXIDATIVE STRESS, METABOLIC DISEASE, COA KEYWDS 2 BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR Y.L.BOERSMA,J.NEWMAN,T.E.ADAMS,L.SPARROW,N.COWIESON,D.LUCENT, AUTHOR 2 G.KRIPPNER,K.BOZAOGLU,T.S.PEAT REVDAT 5 20-DEC-23 4CYY 1 HETSYN REVDAT 4 29-JUL-20 4CYY 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 08-MAY-19 4CYY 1 REMARK LINK REVDAT 2 25-FEB-15 4CYY 1 JRNL REVDAT 1 10-DEC-14 4CYY 0 JRNL AUTH Y.L.BOERSMA,J.NEWMAN,T.E.ADAMS,N.COWIESON,G.KRIPPNER, JRNL AUTH 2 K.BOZAOGLU,T.S.PEAT JRNL TITL THE STRUCTURE OF VANIN-1: A KEY ENZYME LINKING METABOLIC JRNL TITL 2 DISEASE AND INFLAMMATION JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 3320 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 25478849 JRNL DOI 10.1107/S1399004714022767 REMARK 2 REMARK 2 RESOLUTION. 2.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0069 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 88.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 17545 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 947 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.89 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1226 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.3880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3615 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 11 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.84000 REMARK 3 B22 (A**2) : 2.84000 REMARK 3 B33 (A**2) : -9.23000 REMARK 3 B12 (A**2) : 1.42000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.600 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.296 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.231 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.219 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3803 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3459 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5184 ; 1.322 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7953 ; 0.710 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 459 ; 7.031 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;36.198 ;24.682 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 583 ;15.288 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;18.372 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 585 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4293 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 876 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1842 ; 2.677 ; 5.844 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1841 ; 2.675 ; 5.843 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2299 ; 4.309 ; 8.760 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1961 ; 3.816 ; 6.527 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 4CYY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-14. REMARK 100 THE DEPOSITION ID IS D_1290060365. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95370 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 : 18526 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.890 REMARK 200 RESOLUTION RANGE LOW (A) : 47.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 16.30 REMARK 200 R MERGE (I) : 0.21000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 16.10 REMARK 200 R MERGE FOR SHELL (I) : 1.12000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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 4CYF REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PROTEIN WAS AT 15 MG/ML. THE REMARK 280 RESERVOIR CONDITIONS WERE 25% (W/V) PEG 1500 PLUS 10% (V/V) REMARK 280 SUCCINATE-PHOSPHATE-GLYCINE BUFFER AT PH 6.0. THE PLATES WERE REMARK 280 SET UP AT 8 C AND THE DROPS WERE 150 NL PLUS 150 NL IN SITTING REMARK 280 DROP PLATES., VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 89.10133 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 44.55067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.55067 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 89.10133 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 ALA A 8 REMARK 465 SER A 9 REMARK 465 ILE A 10 REMARK 465 SER A 11 REMARK 465 ALA A 12 REMARK 465 ARG A 13 REMARK 465 ASP A 14 REMARK 465 TYR A 15 REMARK 465 LYS A 16 REMARK 465 ASP A 17 REMARK 465 ASP A 18 REMARK 465 ASP A 19 REMARK 465 ASN A 113 REMARK 465 ARG A 114 REMARK 465 PHE A 115 REMARK 465 TRP A 484 REMARK 465 ALA A 485 REMARK 465 SER A 486 REMARK 465 ASN A 487 REMARK 465 ALA A 488 REMARK 465 SER A 489 REMARK 465 SER A 490 REMARK 465 GLY A 491 REMARK 465 LEU A 492 REMARK 465 THR A 493 REMARK 465 ALA A 494 REMARK 465 GLN A 495 REMARK 465 ALA A 496 REMARK 465 ARG A 497 REMARK 465 ILE A 498 REMARK 465 ILE A 499 REMARK 465 MET A 500 REMARK 465 LEU A 501 REMARK 465 ILE A 502 REMARK 465 VAL A 503 REMARK 465 ILE A 504 REMARK 465 ALA A 505 REMARK 465 PRO A 506 REMARK 465 ILE A 507 REMARK 465 VAL A 508 REMARK 465 CYS A 509 REMARK 465 SER A 510 REMARK 465 LEU A 511 REMARK 465 SER A 512 REMARK 465 TRP A 513 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 ASP A 20 CG OD1 OD2 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 OG SER A 455 OD1 ASP A 457 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 PRO A 43 134.59 -35.42 REMARK 500 ASN A 105 75.92 66.69 REMARK 500 ASN A 111 70.04 -114.75 REMARK 500 THR A 118 57.37 -148.53 REMARK 500 GLU A 185 38.09 -83.38 REMARK 500 CYS A 211 -110.43 38.70 REMARK 500 TYR A 269 79.08 -157.07 REMARK 500 SER A 271 -33.95 -36.49 REMARK 500 THR A 275 142.78 179.96 REMARK 500 SER A 302 141.30 -170.28 REMARK 500 LYS A 359 -114.21 49.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CYF RELATED DB: PDB REMARK 900 THE STRUCTURE OF VANIN-1: DEFINING THE LINK BETWEEN METABOLIC REMARK 900 DISEASE, OXIDATIVE STRESS AND INFLAMMATION REMARK 900 RELATED ID: 4CYG RELATED DB: PDB REMARK 900 THE STRUCTURE OF VANIN-1: DEFINING THE LINK BETWEEN METABOLIC REMARK 900 DISEASE, OXIDATIVE STRESS AND INFLAMMATION REMARK 900 RELATED ID: 4CYU RELATED DB: PDB REMARK 900 STAPHYLOCOCCUS AUREUS 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN- REMARK 900 PYROPHOSPHOKINASE IN COMPLEX WITH AMPCPP REMARK 999 REMARK 999 SEQUENCE REMARK 999 FLAG TAG AT N-TERMINUS AND THE PRO-PEPTIDE AT THE C- REMARK 999 TERMINUS HAS BEEN REMOVED TO GIVE THE MATURE FORM OF THE REMARK 999 PROTEIN. IN ADDITION THE DEPOSITED STRUCTURE HAS THE REMARK 999 NATURALLY OCCURRING THR26ILE SNP IN THE SEQUENCE. DBREF 4CYY A 27 513 UNP O95497 VNN1_HUMAN 27 513 SEQADV 4CYY ALA A 8 UNP O95497 EXPRESSION TAG SEQADV 4CYY SER A 9 UNP O95497 EXPRESSION TAG SEQADV 4CYY ILE A 10 UNP O95497 EXPRESSION TAG SEQADV 4CYY SER A 11 UNP O95497 EXPRESSION TAG SEQADV 4CYY ALA A 12 UNP O95497 EXPRESSION TAG SEQADV 4CYY ARG A 13 UNP O95497 EXPRESSION TAG SEQADV 4CYY ASP A 14 UNP O95497 EXPRESSION TAG SEQADV 4CYY TYR A 15 UNP O95497 EXPRESSION TAG SEQADV 4CYY LYS A 16 UNP O95497 EXPRESSION TAG SEQADV 4CYY ASP A 17 UNP O95497 EXPRESSION TAG SEQADV 4CYY ASP A 18 UNP O95497 EXPRESSION TAG SEQADV 4CYY ASP A 19 UNP O95497 EXPRESSION TAG SEQADV 4CYY ASP A 20 UNP O95497 EXPRESSION TAG SEQADV 4CYY LYS A 21 UNP O95497 EXPRESSION TAG SEQADV 4CYY GLN A 22 UNP O95497 EXPRESSION TAG SEQADV 4CYY ASP A 23 UNP O95497 EXPRESSION TAG SEQADV 4CYY THR A 24 UNP O95497 EXPRESSION TAG SEQADV 4CYY PHE A 25 UNP O95497 EXPRESSION TAG SEQADV 4CYY ILE A 26 UNP O95497 EXPRESSION TAG SEQRES 1 A 506 ALA SER ILE SER ALA ARG ASP TYR LYS ASP ASP ASP ASP SEQRES 2 A 506 LYS GLN ASP THR PHE ILE ALA ALA VAL TYR GLU HIS ALA SEQRES 3 A 506 ALA ILE LEU PRO ASN ALA THR LEU THR PRO VAL SER ARG SEQRES 4 A 506 GLU GLU ALA LEU ALA LEU MET ASN ARG ASN LEU ASP ILE SEQRES 5 A 506 LEU GLU GLY ALA ILE THR SER ALA ALA ASP GLN GLY ALA SEQRES 6 A 506 HIS ILE ILE VAL THR PRO GLU ASP ALA ILE TYR GLY TRP SEQRES 7 A 506 ASN PHE ASN ARG ASP SER LEU TYR PRO TYR LEU GLU ASP SEQRES 8 A 506 ILE PRO ASP PRO GLU VAL ASN TRP ILE PRO CYS ASN ASN SEQRES 9 A 506 ARG ASN ARG PHE GLY GLN THR PRO VAL GLN GLU ARG LEU SEQRES 10 A 506 SER CYS LEU ALA LYS ASN ASN SER ILE TYR VAL VAL ALA SEQRES 11 A 506 ASN ILE GLY ASP LYS LYS PRO CYS ASP THR SER ASP PRO SEQRES 12 A 506 GLN CYS PRO PRO ASP GLY ARG TYR GLN TYR ASN THR ASP SEQRES 13 A 506 VAL VAL PHE ASP SER GLN GLY LYS LEU VAL ALA ARG TYR SEQRES 14 A 506 HIS LYS GLN ASN LEU PHE MET GLY GLU ASN GLN PHE ASN SEQRES 15 A 506 VAL PRO LYS GLU PRO GLU ILE VAL THR PHE ASN THR THR SEQRES 16 A 506 PHE GLY SER PHE GLY ILE PHE THR CYS PHE ASP ILE LEU SEQRES 17 A 506 PHE HIS ASP PRO ALA VAL THR LEU VAL LYS ASP PHE HIS SEQRES 18 A 506 VAL ASP THR ILE VAL PHE PRO THR ALA TRP MET ASN VAL SEQRES 19 A 506 LEU PRO HIS LEU SER ALA VAL GLU PHE HIS SER ALA TRP SEQRES 20 A 506 ALA MET GLY MET ARG VAL ASN PHE LEU ALA SER ASN ILE SEQRES 21 A 506 HIS TYR PRO SER LYS LYS MET THR GLY SER GLY ILE TYR SEQRES 22 A 506 ALA PRO ASN SER SER ARG ALA PHE HIS TYR ASP MET LYS SEQRES 23 A 506 THR GLU GLU GLY LYS LEU LEU LEU SER GLN LEU ASP SER SEQRES 24 A 506 HIS PRO SER HIS SER ALA VAL VAL ASN TRP THR SER TYR SEQRES 25 A 506 ALA SER SER ILE GLU ALA LEU SER SER GLY ASN LYS GLU SEQRES 26 A 506 PHE LYS GLY THR VAL PHE PHE ASP GLU PHE THR PHE VAL SEQRES 27 A 506 LYS LEU THR GLY VAL ALA GLY ASN TYR THR VAL CYS GLN SEQRES 28 A 506 LYS ASP LEU CYS CYS HIS LEU SER TYR LYS MET SER GLU SEQRES 29 A 506 ASN ILE PRO ASN GLU VAL TYR ALA LEU GLY ALA PHE ASP SEQRES 30 A 506 GLY LEU HIS THR VAL GLU GLY ARG TYR TYR LEU GLN ILE SEQRES 31 A 506 CYS THR LEU LEU LYS CYS LYS THR THR ASN LEU ASN THR SEQRES 32 A 506 CYS GLY ASP SER ALA GLU THR ALA SER THR ARG PHE GLU SEQRES 33 A 506 MET PHE SER LEU SER GLY THR PHE GLY THR GLN TYR VAL SEQRES 34 A 506 PHE PRO GLU VAL LEU LEU SER GLU ASN GLN LEU ALA PRO SEQRES 35 A 506 GLY GLU PHE GLN VAL SER THR ASP GLY ARG LEU PHE SER SEQRES 36 A 506 LEU LYS PRO THR SER GLY PRO VAL LEU THR VAL THR LEU SEQRES 37 A 506 PHE GLY ARG LEU TYR GLU LYS ASP TRP ALA SER ASN ALA SEQRES 38 A 506 SER SER GLY LEU THR ALA GLN ALA ARG ILE ILE MET LEU SEQRES 39 A 506 ILE VAL ILE ALA PRO ILE VAL CYS SER LEU SER TRP MODRES 4CYY ASN A 38 ASN GLYCOSYLATION SITE MODRES 4CYY ASN A 130 ASN GLYCOSYLATION SITE MODRES 4CYY ASN A 200 ASN GLYCOSYLATION SITE MODRES 4CYY ASN A 315 ASN GLYCOSYLATION SITE MODRES 4CYY ASN A 353 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG A 522 14 HET NAG A 525 14 HET NAG A 532 14 HET NAG A 533 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 6(C8 H15 N O6) FORMUL 7 HOH *11(H2 O) HELIX 1 1 SER A 45 ASP A 69 1 25 HELIX 2 2 ASN A 88 TYR A 93 1 6 HELIX 3 3 PRO A 94 LEU A 96 5 3 HELIX 4 4 ASP A 101 ASN A 105 5 5 HELIX 5 5 THR A 118 ASN A 131 1 14 HELIX 6 6 THR A 210 PHE A 216 5 7 HELIX 7 7 PRO A 219 ASP A 226 1 8 HELIX 8 8 SER A 246 ARG A 259 1 14 HELIX 9 9 PRO A 270 LYS A 273 5 4 HELIX 10 10 THR A 317 SER A 322 1 6 HELIX 11 11 ASN A 407 CYS A 411 5 5 HELIX 12 12 TYR A 480 ASP A 483 5 4 SHEET 1 AA 6 LEU A 172 HIS A 177 0 SHEET 2 AA 6 ARG A 157 PHE A 166 -1 O ASP A 163 N TYR A 176 SHEET 3 AA 6 TYR A 134 PRO A 144 -1 O VAL A 135 N PHE A 166 SHEET 4 AA 6 ILE A 74 VAL A 76 1 O ILE A 75 N VAL A 136 SHEET 5 AA 6 THR A 24 GLU A 31 1 O ALA A 28 N VAL A 76 SHEET 6 AA 6 LYS A 298 ASP A 305 -1 O LYS A 298 N GLU A 31 SHEET 1 AB 6 THR A 198 THR A 201 0 SHEET 2 AB 6 GLY A 204 ILE A 208 -1 O GLY A 204 N THR A 201 SHEET 3 AB 6 THR A 231 PRO A 235 1 O THR A 231 N GLY A 207 SHEET 4 AB 6 ASN A 261 SER A 265 1 O ASN A 261 N ILE A 232 SHEET 5 AB 6 SER A 277 TYR A 280 -1 O GLY A 278 N ALA A 264 SHEET 6 AB 6 SER A 285 HIS A 289 -1 N ARG A 286 O ILE A 279 SHEET 1 AC 6 GLU A 332 VAL A 337 0 SHEET 2 AC 6 ASP A 340 LEU A 347 -1 O ASP A 340 N VAL A 337 SHEET 3 AC 6 TYR A 378 HIS A 387 -1 O TYR A 378 N LEU A 347 SHEET 4 AC 6 TYR A 393 LYS A 402 -1 O TYR A 393 N HIS A 387 SHEET 5 AC 6 VAL A 470 ARG A 478 -1 O LEU A 471 N LYS A 402 SHEET 6 AC 6 VAL A 436 LEU A 442 -1 O PHE A 437 N PHE A 476 SHEET 1 AD 5 ALA A 351 GLN A 358 0 SHEET 2 AD 5 LEU A 361 MET A 369 -1 O LEU A 361 N GLN A 358 SHEET 3 AD 5 PHE A 422 GLY A 429 -1 N GLU A 423 O LYS A 368 SHEET 4 AD 5 LEU A 460 SER A 462 -1 O LEU A 460 N LEU A 427 SHEET 5 AD 5 PHE A 452 VAL A 454 -1 O GLN A 453 N PHE A 461 SSBOND 1 CYS A 109 CYS A 126 1555 1555 2.08 SSBOND 2 CYS A 145 CYS A 152 1555 1555 2.06 SSBOND 3 CYS A 363 CYS A 398 1555 1555 2.05 SSBOND 4 CYS A 403 CYS A 411 1555 1555 2.05 LINK ND2 ASN A 38 C1 NAG A 532 1555 1555 1.46 LINK ND2 ASN A 130 C1 NAG A 533 1555 1555 1.46 LINK ND2 ASN A 200 C1 NAG B 1 1555 1555 1.43 LINK ND2 ASN A 315 C1 NAG A 522 1555 1555 1.46 LINK ND2 ASN A 353 C1 NAG A 525 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 CISPEP 1 ASN A 111 ARG A 112 0 -5.21 CISPEP 2 ASP A 218 PRO A 219 0 1.50 CISPEP 3 LEU A 242 PRO A 243 0 -0.64 CRYST1 101.904 101.904 133.652 90.00 90.00 120.00 P 32 2 1 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 0.009813 0.005666 0.000000 0.00000 SCALE2 0.000000 0.011331 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007482 0.00000