HEADER DNA BINDING PROTEIN 15-APR-10 2KWQ TITLE MCM10 C-TERMINAL DNA BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN MCM10 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DNA BINDING DOMAIN (UNP RESIDUES 755-842); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 GENE: MCM10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET32A-PPS KEYWDS MCM10, DNA REPLICATION, DNA BINDING, ZINC MOTIF, ZINC RIBBON, DNA KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.D.ROBERTSON,B.CHAGOT,W.J.CHAZIN,B.F.EICHMAN REVDAT 4 14-JUN-23 2KWQ 1 REMARK LINK REVDAT 3 05-FEB-20 2KWQ 1 REMARK SEQADV REVDAT 2 11-AUG-10 2KWQ 1 JRNL REVDAT 1 19-MAY-10 2KWQ 0 JRNL AUTH P.D.ROBERTSON,B.CHAGOT,W.J.CHAZIN,B.F.EICHMAN JRNL TITL SOLUTION NMR STRUCTURE OF THE C-TERMINAL DNA BINDING DOMAIN JRNL TITL 2 OF MCM10 REVEALS A CONSERVED MCM MOTIF. JRNL REF J.BIOL.CHEM. V. 285 22942 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20489205 JRNL DOI 10.1074/JBC.M110.131276 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, AMBER REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), CASE, REMARK 3 DARDEN, CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, REMARK 3 ... AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MOLECULAR DYNAMICS REMARK 4 REMARK 4 2KWQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000101668. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 920 UM [U-100% 15N] ENTITY_1-1, REMARK 210 25 MM SODIUM PHOSPHATE-2, 100 MM REMARK 210 SODIUM CHLORIDE-3, 5 % D2O-4, 95 REMARK 210 % H2O-5, 95% H2O/5% D2O; 300 UM REMARK 210 [U-100% 15N] ENTITY_1-6, 25 MM REMARK 210 SODIUM PHOSPHATE-7, 100 MM REMARK 210 SODIUM CHLORIDE-8, 5 % D2O-9, 95 REMARK 210 % H2O-10, 95% H2O/5% D2O; 920 UM REMARK 210 [U-100% 13C] ENTITY_1-11, 25 MM REMARK 210 SODIUM PHOSPHATE-12, 100 MM REMARK 210 SODIUM CHLORIDE-13, 5 % D2O-14, REMARK 210 95 % H2O-15, 95% H2O/5% D2O; 920 REMARK 210 UM [U-100% 13C; U-100% 15N] REMARK 210 ENTITY_1-16, 25 MM SODIUM REMARK 210 PHOSPHATE-17, 100 MM SODIUM REMARK 210 CHLORIDE-18, 5 % D2O-19, 95 % REMARK 210 H2O-20, 95% H2O/5% D2O; 920 UM REMARK 210 ENTITY_1-21, 25 MM SODIUM REMARK 210 PHOSPHATE-22, 100 MM SODIUM REMARK 210 CHLORIDE-23, 5 % D2O-24, 95 % REMARK 210 H2O-25, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-1H COSY; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D HNCACB; 3D HBHA(CO)NH; REMARK 210 3D HNHA; 3D H(CCO)NH; 3D C(CO)NH; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D (HB)CB(CGCD)HD REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, TOPSPIN, TALOS REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 2 ARG A 828 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 828 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG A 828 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG A 797 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 828 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A 759 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 6 ARG A 759 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 6 ARG A 806 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 828 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 828 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 828 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 797 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 ARG A 797 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 13 ARG A 828 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 15 ARG A 797 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 797 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 17 ARG A 828 NE - CZ - NH1 ANGL. DEV. = 3.4 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 ARG A 759 12.62 -61.73 REMARK 500 1 ASN A 786 45.17 70.06 REMARK 500 1 LYS A 825 31.26 -145.55 REMARK 500 2 MET A -2 170.98 175.18 REMARK 500 2 LYS A 825 30.18 -140.33 REMARK 500 3 GLN A 756 -37.56 73.04 REMARK 500 3 ARG A 759 38.92 -72.10 REMARK 500 3 ARG A 812 1.00 -69.07 REMARK 500 3 THR A 836 137.56 89.39 REMARK 500 4 ARG A 759 46.91 -76.56 REMARK 500 4 LYS A 825 31.57 -143.13 REMARK 500 5 GLN A 756 -25.42 84.89 REMARK 500 5 ARG A 759 29.21 -77.27 REMARK 500 5 LYS A 825 31.22 -146.46 REMARK 500 6 LYS A 772 65.79 72.07 REMARK 500 6 LYS A 825 30.93 -145.49 REMARK 500 7 PRO A 814 176.93 -59.28 REMARK 500 7 HIS A 817 152.47 71.60 REMARK 500 7 LYS A 825 29.16 -146.80 REMARK 500 8 ARG A 759 21.15 -70.48 REMARK 500 8 LYS A 772 34.53 70.24 REMARK 500 9 SER A 757 89.63 -174.16 REMARK 500 9 ASN A 786 43.69 70.50 REMARK 500 10 MET A 755 32.72 -84.48 REMARK 500 10 SER A 757 -103.03 -87.79 REMARK 500 10 HIS A 792 -167.02 -164.92 REMARK 500 10 LYS A 825 29.36 -144.85 REMARK 500 11 LYS A 772 6.80 85.76 REMARK 500 11 LYS A 825 33.63 -141.04 REMARK 500 11 LEU A 832 -137.55 -150.67 REMARK 500 11 LYS A 835 -66.77 63.40 REMARK 500 11 THR A 836 -41.75 70.15 REMARK 500 12 ARG A 759 42.30 -76.98 REMARK 500 12 LYS A 825 27.21 -144.05 REMARK 500 13 MET A -2 -27.21 72.29 REMARK 500 13 MET A 755 -29.30 72.73 REMARK 500 13 ARG A 759 23.19 -71.11 REMARK 500 13 LYS A 825 29.32 -145.17 REMARK 500 13 MET A 831 115.77 -163.20 REMARK 500 14 ARG A 759 34.83 -71.02 REMARK 500 14 LYS A 825 31.53 -141.82 REMARK 500 15 ARG A 759 20.57 -70.10 REMARK 500 15 LYS A 825 30.64 -141.65 REMARK 500 16 GLN A 756 -44.59 135.30 REMARK 500 16 ARG A 759 37.92 -79.98 REMARK 500 16 LYS A 772 30.87 71.47 REMARK 500 16 ASN A 786 49.43 70.82 REMARK 500 16 LYS A 825 31.13 -140.23 REMARK 500 17 ARG A 759 7.32 -66.06 REMARK 500 17 LYS A 772 35.57 73.14 REMARK 500 REMARK 500 THIS ENTRY HAS 60 RAMACHANDRAN OUTLIERS. 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 GLU A 760 GLN A 761 17 -148.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 843 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 768 SG REMARK 620 2 CYS A 771 SG 111.6 REMARK 620 3 CYS A 782 SG 120.8 122.2 REMARK 620 4 HIS A 787 ND1 103.7 93.9 95.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 844 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 801 SG REMARK 620 2 CYS A 803 SG 105.9 REMARK 620 3 CYS A 818 SG 111.0 113.6 REMARK 620 4 CYS A 821 SG 116.4 109.1 101.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 843 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 844 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16872 RELATED DB: BMRB DBREF 2KWQ A 755 842 UNP Q5EAW4 MCM10_XENLA 755 842 SEQADV 2KWQ GLY A -4 UNP Q5EAW4 EXPRESSION TAG SEQADV 2KWQ PRO A -3 UNP Q5EAW4 EXPRESSION TAG SEQADV 2KWQ MET A -2 UNP Q5EAW4 EXPRESSION TAG SEQADV 2KWQ GLY A -1 UNP Q5EAW4 EXPRESSION TAG SEQRES 1 A 92 GLY PRO MET GLY MET GLN SER ILE ARG GLU GLN SER CYS SEQRES 2 A 92 ARG VAL VAL THR CYS LYS THR CYS LYS TYR THR HIS PHE SEQRES 3 A 92 LYS PRO LYS GLU THR CYS VAL SER GLU ASN HIS ASP PHE SEQRES 4 A 92 HIS TRP HIS ASN GLY VAL LYS ARG PHE PHE LYS CYS PRO SEQRES 5 A 92 CYS GLY ASN ARG THR ILE SER LEU ASP ARG LEU PRO LYS SEQRES 6 A 92 LYS HIS CYS SER THR CYS GLY LEU PHE LYS TRP GLU ARG SEQRES 7 A 92 VAL GLY MET LEU LYS GLU LYS THR GLY PRO LYS LEU GLY SEQRES 8 A 92 GLY HET ZN A 843 1 HET ZN A 844 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 LYS A 779 GLU A 785 1 7 SHEET 1 A 3 THR A 774 HIS A 775 0 SHEET 2 A 3 SER A 762 CYS A 768 -1 N VAL A 766 O HIS A 775 SHEET 3 A 3 PHE A 789 VAL A 795 -1 O HIS A 792 N VAL A 765 SHEET 1 B 3 ARG A 806 SER A 809 0 SHEET 2 B 3 ARG A 797 LYS A 800 -1 N ARG A 797 O SER A 809 SHEET 3 B 3 GLU A 827 VAL A 829 -1 O VAL A 829 N PHE A 798 LINK SG CYS A 768 ZN ZN A 843 1555 1555 2.48 LINK SG CYS A 771 ZN ZN A 843 1555 1555 2.45 LINK SG CYS A 782 ZN ZN A 843 1555 1555 2.47 LINK ND1 HIS A 787 ZN ZN A 843 1555 1555 2.22 LINK SG CYS A 801 ZN ZN A 844 1555 1555 2.35 LINK SG CYS A 803 ZN ZN A 844 1555 1555 2.41 LINK SG CYS A 818 ZN ZN A 844 1555 1555 2.41 LINK SG CYS A 821 ZN ZN A 844 1555 1555 2.41 CISPEP 1 GLY A -1 MET A 755 1 3.45 CISPEP 2 GLY A -1 MET A 755 2 3.66 CISPEP 3 GLY A 837 PRO A 838 19 -24.84 SITE 1 AC1 5 CYS A 768 CYS A 771 TYR A 773 CYS A 782 SITE 2 AC1 5 HIS A 787 SITE 1 AC2 4 CYS A 801 CYS A 803 CYS A 818 CYS A 821 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