HEADER HYDROLASE 08-JUN-10 2KYT TITLE SOLUTION STRUCTURE OF THE H-REV107 N-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROUP XVI PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-125; COMPND 5 SYNONYM: ADIPOSE-SPECIFIC PHOSPHOLIPASE A2, ADPLA, HRAS-LIKE COMPND 6 SUPPRESSOR 3, H-REV 107 PROTEIN HOMOLOG, HREV107-3, RENAL CARCINOMA COMPND 7 ANTIGEN NY-REN-65; COMPND 8 EC: 3.1.1.4; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PLA2G16, HRASLS3, HREV107; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET24A KEYWDS H-REV107, TUMOR SUPPRESSOR, PHOSPHOLIPASE, N-TERMINAL DOMAIN, KEYWDS 2 HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR X.REN,B.XIA REVDAT 3 01-MAY-24 2KYT 1 REMARK REVDAT 2 21-DEC-16 2KYT 1 TITLE VERSN REVDAT 1 03-NOV-10 2KYT 0 JRNL AUTH X.REN,J.LIN,C.JIN,B.XIA JRNL TITL SOLUTION STRUCTURE OF THE N-TERMINAL CATALYTIC DOMAIN OF JRNL TITL 2 HUMAN H-REV107--A NOVEL CIRCULAR PERMUTATED NLPC/P60 DOMAIN JRNL REF FEBS LETT. V. 584 4222 2010 JRNL REFN ISSN 0014-5793 JRNL PMID 20837014 JRNL DOI 10.1016/J.FEBSLET.2010.09.015 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.1, AMBER REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), CASE, DARDEN, CHEATHAM, III, SIMMERLING, REMARK 3 WANG, DUKE, LUO, AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KYT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000101743. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 60 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] H-REV107N-1, REMARK 210 30 MM SODIUM PHOSPHATE-2, 30 MM REMARK 210 SODIUM CHLORIDE-3, 10 MM DTT-4, REMARK 210 90 % H2O-5, 10 % D2O-6, 0.05 W/V REMARK 210 SODIUM AZIDE-7, 0.02 W/V DSS-8, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D HCCH-TOCSY; 3D HBHA(CO) REMARK 210 NH; 3D HCCH-COSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 5, XWINNMR 3.5, TOPSPIN REMARK 210 2.1, MOLMOL, CYANA, AMBER, TALOS, REMARK 210 PROCHECKNMR, SANE REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 5 TYR A 122 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 12 TYR A 122 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 13 TYR A 122 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 14 TYR A 122 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 15 ARG A 22 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES 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 1 TYR A 21 -155.89 -159.40 REMARK 500 1 PRO A 39 103.83 -53.67 REMARK 500 1 VAL A 42 -21.79 -140.62 REMARK 500 1 ALA A 45 27.78 49.68 REMARK 500 1 ALA A 47 17.36 -142.68 REMARK 500 1 SER A 49 -8.71 -59.89 REMARK 500 1 ASP A 72 -50.80 -165.79 REMARK 500 1 ASN A 77 75.06 -154.09 REMARK 500 1 ASN A 78 94.89 -67.45 REMARK 500 1 LYS A 83 -41.14 -132.30 REMARK 500 1 SER A 85 72.16 -178.78 REMARK 500 1 LEU A 105 42.09 -103.33 REMARK 500 2 ILE A 5 55.63 37.02 REMARK 500 2 TYR A 21 -169.00 -162.58 REMARK 500 2 VAL A 42 -130.13 42.39 REMARK 500 2 ALA A 45 17.90 56.98 REMARK 500 2 VAL A 50 107.79 -52.81 REMARK 500 2 MET A 51 22.07 49.69 REMARK 500 2 SER A 52 13.44 -146.20 REMARK 500 2 ASP A 72 -56.11 -165.04 REMARK 500 2 ASN A 77 67.96 -150.63 REMARK 500 2 HIS A 80 43.47 -163.11 REMARK 500 2 SER A 85 66.28 -164.82 REMARK 500 3 PRO A 4 -166.81 -70.12 REMARK 500 3 ILE A 5 54.80 -115.09 REMARK 500 3 TYR A 21 -165.86 -161.68 REMARK 500 3 VAL A 50 -39.66 69.46 REMARK 500 3 ASP A 56 20.28 -144.11 REMARK 500 3 ASP A 72 -67.90 -162.76 REMARK 500 3 ASN A 77 55.42 -147.30 REMARK 500 3 LYS A 83 -25.02 -143.20 REMARK 500 3 SER A 85 72.52 165.64 REMARK 500 4 GLU A 7 30.70 -146.54 REMARK 500 4 PHE A 20 13.05 -140.97 REMARK 500 4 ASP A 30 41.77 -77.35 REMARK 500 4 ASP A 72 -59.70 -162.26 REMARK 500 4 ASN A 77 70.78 -153.37 REMARK 500 4 ASP A 81 23.92 -73.11 REMARK 500 4 LYS A 83 -31.59 -132.82 REMARK 500 4 TYR A 84 136.11 67.81 REMARK 500 5 ARG A 2 -39.15 65.51 REMARK 500 5 GLU A 7 52.07 -160.46 REMARK 500 5 TYR A 21 -165.83 -163.02 REMARK 500 5 SER A 40 -164.21 53.13 REMARK 500 5 VAL A 42 -41.06 69.77 REMARK 500 5 ASP A 72 -61.42 -159.08 REMARK 500 5 ASN A 77 68.55 -158.74 REMARK 500 5 ASN A 78 101.58 -59.91 REMARK 500 5 TYR A 84 -156.09 -136.37 REMARK 500 6 GLU A 7 75.14 -168.87 REMARK 500 REMARK 500 THIS ENTRY HAS 181 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 9 ARG A 22 0.13 SIDE CHAIN REMARK 500 12 ARG A 121 0.09 SIDE CHAIN REMARK 500 14 ARG A 22 0.12 SIDE CHAIN REMARK 500 15 ARG A 121 0.10 SIDE CHAIN REMARK 500 16 TYR A 66 0.09 SIDE CHAIN REMARK 500 17 ARG A 22 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16883 RELATED DB: BMRB DBREF 2KYT A 1 125 UNP P53816 PAG16_HUMAN 1 125 SEQRES 1 A 125 MET ARG ALA PRO ILE PRO GLU PRO LYS PRO GLY ASP LEU SEQRES 2 A 125 ILE GLU ILE PHE ARG PRO PHE TYR ARG HIS TRP ALA ILE SEQRES 3 A 125 TYR VAL GLY ASP GLY TYR VAL VAL HIS LEU ALA PRO PRO SEQRES 4 A 125 SER GLU VAL ALA GLY ALA GLY ALA ALA SER VAL MET SER SEQRES 5 A 125 ALA LEU THR ASP LYS ALA ILE VAL LYS LYS GLU LEU LEU SEQRES 6 A 125 TYR ASP VAL ALA GLY SER ASP LYS TYR GLN VAL ASN ASN SEQRES 7 A 125 LYS HIS ASP ASP LYS TYR SER PRO LEU PRO CYS SER LYS SEQRES 8 A 125 ILE ILE GLN ARG ALA GLU GLU LEU VAL GLY GLN GLU VAL SEQRES 9 A 125 LEU TYR LYS LEU THR SER GLU ASN CYS GLU HIS PHE VAL SEQRES 10 A 125 ASN GLU LEU ARG TYR GLY VAL ALA HELIX 1 1 ALA A 48 ALA A 53 5 6 HELIX 2 2 LEU A 65 ALA A 69 1 5 HELIX 3 3 GLY A 70 ASP A 72 5 3 HELIX 4 4 PRO A 88 VAL A 100 1 13 HELIX 5 5 THR A 109 GLY A 123 1 15 SHEET 1 A 6 LYS A 73 VAL A 76 0 SHEET 2 A 6 LEU A 13 PHE A 17 -1 N GLU A 15 O GLN A 75 SHEET 3 A 6 ARG A 22 TYR A 27 -1 O ALA A 25 N ILE A 14 SHEET 4 A 6 TYR A 32 ALA A 37 -1 O VAL A 34 N ILE A 26 SHEET 5 A 6 ALA A 58 LEU A 64 -1 O LYS A 61 N HIS A 35 SHEET 6 A 6 GLU A 103 VAL A 104 -1 O VAL A 104 N ALA A 58 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1